sensors
Commentary
Collaborative Use of Sensor Networks and Cyberinfrastructure
to Understand Complex Ecosystem Interactions in a Tropical
Rainforest: Challenges and Lessons Learned
Philip W. Rundel 1, *, Thomas C. Harmon 2 , Angel S. Fernandez-Bou 2,3
Citation: Rundel, P.W.; Harmon, T.C.;
Fernandez-Bou, A.S.; Allen, M.F.
Collaborative Use of Sensor
Networks and Cyberinfrastructure to
Understand Complex Ecosystem
Interactions in a Tropical Rainforest:
Challenges and Lessons Learned.
Sensors 2023, 23, 9081. https://
doi.org/10.3390/s23229081
Academic Editor: Yoshio Inoue
Received: 13 June 2023
Revised: 31 October 2023
Accepted: 6 November 2023
Published: 9 November 2023
Copyright: © 2023 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).
Sensors 2023, 23, 9081. https://doi.org/10.3390/s23229081
and Michael F. Allen 4
1 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
2 Sierra Nevada Research Institute, Department of Civil and Environmental Engineering, University of
California, Merced, CA 95343, USA; tharmon@ucmerced.edu (T.C.H.); afernandezbou@ucsusa.org (A.S.F.-B.)
3 Climate & Energy Program, Union of Concerned Scientists, 500 12th St., Suite 340, Oakland, CA 94607, USA
4 Center for Conservation Biology, Department of Microbiology and Plant Pathology, University of California,
Riverside, CA 92507, USA; mallen@ucr.edu
* Correspondence: rundel@ucla.edu; Tel.: +1-310-971-6340
Abstract: Collaborations between ecosystem ecologists and engineers have led to impressive progress
in developing complex models of biogeochemical fluxes in response to global climate change. Ecology
and engineering iteratively inform and transform each other in these efforts. Nested data streams
from local sources, adjacent networks, and remote sensing sources together magnify the capacity of
ecosystem ecologists to observe systems in near real-time and address questions at temporal and
spatial scales that were previously unobtainable. We describe our research experiences working
in a Costa Rican rainforest ecosystem with the challenges presented by constant high humidity,
4300 mm of annual rainfall, flooding, small invertebrates entering the tiniest openings, stinging
insects, and venomous snakes. Over the past two decades, we faced multiple challenges and
learned from our mistakes to develop a broad program of ecosystem research at multiple levels of
integration. This program involved integrated networks of diverse sensors on a series of canopy
towers linked to multiple belowground soil sensor arrays that could transport sensor data streams
from the forest directly to an off-site location via a fiber optic cable. In our commentary, we highlight
three components of our work: (1) the eddy flux measurements using canopy towers; (2) the soil
sensor arrays for measuring the spatial and temporal patterns of CO2 and O2 fluxes at the soil–
atmosphere interface; and (3) focused investigations of the ecosystem impact of leaf-cutter ants as
“ecosystem engineers” on carbon fluxes.
Keywords: tropical forest; global change; carbon cycle; eddy covariance; soil fluxes; leaf-cutter ants;
research challenges
1. Introduction
Sensor networks that take advantage of the expanded modalities for sensing capacity
offer exciting advances in the design of powerful sensing arrays with new applications
for ecological and ecosystem research. This progress has allowed for a broadening of
the boundaries of ecosystem and ecological research thanks, in no small part, to the
development of interfaces between environmental science, engineering, and informational
technology. Ongoing advances in understanding the complexities of ecosystem functions
and, importantly, regional and global models for biogeochemical fluxes have been spurred
by the development of new sensor technologies, increased connectivity afforded by the
Internet to transmit and share data, reduced size and weight of sensors, and improved
reliability of environmental sensing hardware under extreme environmental conditions.
Intelligent arrays of sensor networks are emerging as fundamental tools for addressing
complex questions of ecosystem structure and stability in a world with increasing impacts
https://www.mdpi.com/journal/sensors
Sensors 2023, 23, 9081 2 of 16

of global change. The key to these advances has been the innovative application of cyber
infrastructure linking advanced instruments, computing systems, data storage systems, and
repositories [1,2]. These advances often have come, however, with significant challenges,
particularly under extreme environmental conditions.
Sensor networks coupled with associated cyberinfrastructure can provide a powerful
combination of distributed sensing capacity, internet and satellite communication, and com-
putational tools that lend themselves to countless applications in ecological research [3,4].
Moreover, new designs for sensor networks allow for the observation of system fluxes in near
time and real time based on incoming data from local sources, nested or adjacent networks,
and remote sensing data streams. These advances are providing a new and better understand-
ing of dynamic ecological systems by revealing previously unobservable phenomena and by
enhancing the potential for the development of second-generation ecological questions that we
have not yet addressed [4].
Additionally, new observational and experimental advancements are available for
the first time, enabling scientists to address challenging questions using enhanced spatial
and temporal sampling. These powerful innovations can deliver: (1) full four-dimensional
access to the environment with long-lived, continuously operating, stationary and mobile
sensor nodes suspended in the forest canopy; (2) self-organized, standards-based, broad-
band wireless networks and software systems, permitting broadband access to sensor
nodes; and (3) the integration of remote sensor data sources with existing GIS database
assets to provide a comprehensive, continuous, online portal for access to embedded
networked sensor data.

2. Tropical Rainforests as Drivers of Global Change

Although tropical forests cover only about 7% of the land area of the world, they store
one quarter of global terrestrial carbon and account for approx. one-third of global net
primary productivity. Importantly, humid tropical forests in particular play a crucial role
in regulating regional and global climate dynamics [5]. Understanding their responses
to global change is crucial for predicting biogeochemical global carbon and hydrological
cycling. However, the responses of tropical forests to environmental changes are complex
and poorly understood, and important knowledge gaps exist in the development of models
for predicting tropical forest dynamics. There is abundant evidence that global changes
are altering the physical and chemical environment in which tropical trees grow and that
these changes have been occurring for decades across large areas [6]. However, many
of these predictions are based on results from leaf-level studies. How tropical forests
respond and feed back to climate change remains poorly understood at the ecosystem
level [7]. Four critical research questions have been identified as priority needs for policy
makers, conservationists, and ecosystem ecologists. (1) How are dynamic changes in land
use altering the biogeochemical processes in tropical forest ecosystems? (2) How does
the spatial variability in tropical forests impact global change? (3) Are there emergent
trends in the ecosystem responses of tropical forests to global change? (4) What are the key
research and management priorities for tropical forest ecosystems in the context of global
change? [5–9]. These challenges provide critical questions for research and the areas where
the innovative use of sensor arrays can be useful. We briefly describe three areas of sensor
research for our group, which involve linked, spatial, and temporal scales of impact. A
major focus here is not to present the research results from our studies but rather offer a
commentary on the lessons learned and the environmental challenges we faced in working
with sensors and sensor arrays in a wet tropical forest environment.

3. La Selva Biological Station, Costa Rica

Our work involved a mix of traditional and new modalities of networked sensors. In
this commentary, we report on three components of our ongoing research on the biogeo-
chemical cycles of carbon in tropical forest ecosystems, each operating at a different spatial
and temporal scale. The first component involves the use of instrumented canopy towers
Sensors 2023, 23, 9081 3 of 16

for eddy flux measurements. The second describes the development of novel systems of
soil sensor arrays with both environmental monitoring and automated imaging for root
and mycorrhizal fungal growth. The third area of research takes a downscaled approach to
quantify the role of leaf-cutter ants whose life history and behavior as ecosystem engineers
influence the biogeochemical cycles in Neotropical forests. We present brief overviews of
these three areas of research, the multiple challenges in the installation, operation, and
maintenance of the sensors and networked sensor arrays in a wet tropical forest, and the
environmental conditions of high humidity, torrential rains, ubiquitous annoying insects,
venomous snakes, and dynamic forest structures with frequent tree falls.
Our research efforts for the last decade have centered on tropical rainforests at the La
Selva Biological Station, a 1600-hectare reserve of premontane wet forest in the Caribbean
lowlands of northwestern Costa Rica. This field site is extremely wet, averaging 4244 mm
of annual precipitation (1958–2004), with a mean monthly rainfall above 300 mm from May
through December (Figure 1). The peaks of monthly rainfall above 400 mm typically are
present in June–August and November–December, and a drier period occurs from January
through April. Even in the driest period in February and March, however, precipitation
averages above 190 mm each month. There is little seasonal change in the mean monthly
maximum and minimum temperatures. The developed area of La Selva includes more
than 20 buildings with housing and dining for groups or individuals, air-conditioned
laboratories and research buildings, an ambient temperature lab, shade house growth
facilities, and a well-equipped GIS lab serving the research and academic community. The
GIS database contains over 1000 coverages, including aerial photographs, satellite images
(LANDSAT, IKONOS, QuickBird), optical scans (multispectral and hyperspectral), and
active sensor images (RADAR, LiDAR) of La Selva and its broader watershed for several
time periods over the past 45 years. La Selva follows the protocols recommended by
the World Meteorological Organization (WMO) for sensor handling, data collection and
management, and QA/QC [10].

Figure 1. Seasonal climate means for the La Selva Biological Station: (A) The mean daily maximum
(closed circles) and minimum (open circles) air temperatures, and (B) the total monthly precipitation
(vertical bars) and mean daily minimum relative humidity (open triangles) for the La Selva Biological
Station, Costa Rica. The values are the means ± standard errors for each month for the data collected
hourly from 1957 to 2003 for the precipitation, from 1982 to 2003 for the temperature, and from 1992
to 2003 for the relative humidity. Graph courtesy of Eric Graham.
 Sensors 2023, 23, x FOR PEER REVIEW 4 of 17

Figure 1. Seasonal climate means for the La Selva Biological Station: (A) The mean daily maximum
(closed circles) and minimum (open circles) air temperatures, and (B) the total monthly precipitation
Sensors 2023, 23, 9081 (vertical bars) and mean daily minimum relative humidity (open triangles) for the La 4Selva of 16
Biological Station, Costa Rica. The values are the means ± standard errors for each month for the
data collected hourly from 1957 to 2003 for the precipitation, from 1982 to 2003 for the temperature,
and from 1992 to 2003 for the relative humidity. Graph courtesy of Eric Graham.

The La Selva Canopy Tower Network, constructed in 2008 with funding from the U.S.
The La Selva Canopy Tower Network, constructed in 2008 with funding from the
National ScienceU.S.Foundation, consists
National Science of a network
Foundation, consists of ofacanopy
network towers
of canopy intowers
an old-growth
in an old-
forest (Figure 2). growth
They are linked
forest together
(Figure 2). Theyby both
are fiber
linked optic by
together and wireless
both networks,
fiber optic with
and wireless
networks, with
fiber optic and electrical fiber optic and
connections electrical for
extending connections
1 km toextending for 1 km tobuildings.
the laboratory the laboratory
In
buildings. In their original architecture, the scaffolding towers were arranged in a triangle
their original architecture, the scaffolding towers were arranged in a triangle with heights
with heights of 34 m, 42 m, and 51 m, with the two shorter towers connected by a 25-m
of 34 m, 42 m, andwalkway
51 m, with thethe
through two shorter
canopy towers
to provide connected
expanded bytoathe
access 25-m walkway
interior through
tree crowns. The
the canopy to provide
modularexpanded
form of these access
towersto the interior
allows tree
for relative easecrowns. The modular
in reconfiguring the heightform of
(Figure
these towers allows3). for relative ease in reconfiguring the height (Figure 3).

Sensors 2023, 23, x FOR PEER REVIEW Figure 2. Two of the instrumented La Selva canopy towers reaching above the forest canopy.
5 of La
17
Figure 2. Two of the instrumented
Selva La Selva canopy towers reaching above the forest canopy. La Selva
Biological Station.
Biological Station.

Figure 3.3.LaLa
Figure Selva Canopy
Selva TowerTower
Canopy Network. (A) Tower
Network. (A)from below;from
Tower (B) installation
below; (B) of instrumentation
installation of
instrumentation for eddy
for eddy covariance covarianceatmeasurements
measurements the top of the at the top
tower; (C) of the tower;
canopy walkway(C) canopy
betweenwalkway
the two
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aboveLa
the forest
Selva floor. LaStation.
Biological Selva Biological Station.

Underground conduits provide a direct connection of 600-V power and fiber optic
cables from the towers to the laboratory area located 1 km away. An air-conditioned hut
is available near the base of one of the towers to protect the instrumentation requiring
Sensors 2023, 23, 9081 5 of 16

Underground conduits provide a direct connection of 600-V power and fiber optic
cables from the towers to the laboratory area located 1 km away. An air-conditioned hut
is available near the base of one of the towers to protect the instrumentation requiring
temperature and humidity control. Three additional towers consist of triangular radio
(climb-up) towers that provide canopy access points for audio, sensor, or image recording.
The tower footprint offers electricity at both 120 V and 240 V, wireless internet, and cloud
access points.
The bandwidth from the towers to the station is ample (at least 6 mbps) and tied to
the station’s bandwidth out of the station’s 40 mbps capacity. High bandwidth users (e.g.,
high-frequency image files) also have the option of storing their data on station-based
servers and collecting data from the station at low bandwidth use periods or via media
transfer. Internet access has improved in the past 10 years from a 50-kbps telephone line to
40 mbps, including a dedicated line between La Selva and the OTS central offices located
on the research campus of the Universidad de Costa Rica in San José. Internally, the system
is a combination of optical fiber, UTP, and wireless connections.
The data streams from the Canopy Tower Network provide continuous data on
ecosystem fluxes and concurrent detailed canopy and soil environmental conditions as
needed for a broad range of data analyses, syntheses, and modeling efforts (e.g., [11–14]).
The profile system includes sensors for light (PAR), air temperature, and humidity at four
canopy heights (top, upper, middle, and lower canopy). Additional biomet sensors provide
data on the canopy profiles of light and atmospheric conditions that are useful for flux data
analysis and as the input for modeling leaf fluxes using multi-layer ecosystem models. A
strong focus on carbon cycling and global change has developed around the tower facility
(e.g., [15–19]).

4. Eddy Covariance Research

One the best examples of successful efforts to apply new technologies to tropical
forest research came two decades ago with the installation of eddy flux towers within
the Large-scale Biosphere–Atmosphere Experiment (LBA) in Amazonia, an international
research program involving collaborations between hundreds of scientists from Brazil,
the United States, and other countries. Patterned after a previous successful program
of flux studies on boreal ecosystems in Canada, the LBA was motivated by the need for
improved observations of carbon, evapotranspiration, and sensible heat fluxes in the tropics
to understand how changes in land use and climate might affect the sustainability of the
biological and physical functions of Amazonia, as well as their subsequent influence on
the global climate system. The eddy covariance method provides a means to directly and
non-intrusively estimate the vertical transport of CO2 and other greenhouse gases through
and out of the forest canopy. These data, coupled with the appropriate sensors, can provide
invaluable data to improve our understanding of carbon cycles, energy fluxes, and other
atmospheric controls.
The measurements of the net CO2 flux between terrestrial ecosystems and the atmo-
sphere using eddy covariance techniques have been fundamental to the development and
application of global and regional carbon source-sink patterns and predictions of the future
terrestrial carbon balance [11,13,20,21]. The LBA studies suggest that Amazonia has been,
on average, nearly neutral with respect to carbon over the last decade, albeit a small net
source during ENSO events. Despite several decades of eddy flux measurements at multi-
ple sites across the Amazon Basin, regional biogeophysical models have had difficulties in
reproducing the seasonal pattern of the net ecosystem exchange of carbon dioxide. The
eddy covariance measurements of NEE were taken in an old-growth forest.
The global network of eddy covariance towers (FLUXNET) currently consists of more
than 500 active sites, but humid tropical forests are underrepresented [11]. La Selva has
been a flux site since 1998, and past research has identified a large sensitivity of nighttime
temperature fluxes. The daytime net ecosystem fluxes were largely controlled by solar
radiation rather than by evaporative demand. The dry season vapor pressure deficit was
Sensors 2023, 23, 9081 6 of 16

identified as a main control for forest growth on interannual timescales [22–25]. The eddy
covariance research over the last two decades at La Selva has had challenges in maintaining
continuous measurements across the seasons and has further highlighted the challenges of
extrapolating data to broader forest areas.
The eddy covariance analyses carried out from 1984–2000 at La Selva found that
the canopy tree growth in the old-growth forest varied >two-fold among years. The
trees’ annual diameter increments in this 16-yr period were negatively correlated with
the annual means of the daily minimum temperatures [22]. The tree growth variations
were also negatively covaried with the net carbon exchange, as inferred by an inverse
tracer–transport model. The measurements during the 1997–1998 El Niño year found
significant reductions in tree growth, and large inferred tropical releases of CO2 to the
atmosphere occurred. These and other recent findings are consistent with the decreased
net primary production in tropical forests in warm years.
Previously, the walk-up towers at La Selva were similar in height to the scattered
emergent tree crowns. With a new 60-m tower, the eddy covariance system will be located
sufficiently above the mean canopy height to minimize any potential interference of the
tallest trees with the eddy covariance measurements [21]. The canopy profile system will
soon be monitoring light (PAR) and CO2 –H2 O concentrations at 5-m height intervals from
0 m to 50 m. The data from the profile system will be used to calculate the canopy storage
of CO2 , which is an important component of the ecosystem carbon flux budget. Tropical
forests often experience extended periods of very calm air, and under these conditions CO2
can accumulate inside the canopy air space. This has presented a serious challenge in the
past at La Selva. However, the new CO2 profile system should provide novel insights into
the role of carbon storage in creating biases in the ecosystem carbon flux budgets measured
by above-canopy eddy covariance systems.
A team of researchers from UCLA is in the early stages of an NSF project linked with
the eddy covariance towers to carry out an innovative carbonyl sulfide project (NSF funded,
Ulli Seibt, UCLA). The goal of the project is to quantify ecosystem photosynthesis and
respiration for the tropical rainforest at La Selva and link these fluxes to environmental
variations. The researchers will measure ecosystem fluxes of carbonyl sulfide (COS), a
novel tracer of photosynthesis, and obtain estimates of ecosystem photosynthesis from
the COS fluxes. The data will be used in ecosystem modeling to better constrain the
model simulations of tropical photosynthesis. An eddy covariance inlet and automated
chambers will be installed on the height extended tower and will be connected via tubing
to a high-precision COS laser spectrometer housed in the air-conditioned instrument shed.
The shed is critical for high-quality measurements since the laser spectrometer is sensitive
to temperature fluctuations.

5. Soil Sensor Arrays

Tropical rainforest soils receive large inputs of carbon from the atmosphere through
photosynthesis. However, organic matter decomposition is also very high as moisture
and temperature are optimal for microbial growth and turnover, releasing that carbon
back to the atmosphere. The primary limitation is presumed to be nutrients due to high
leaching rates and saturated moisture levels that restrict O2 for aerobic microbial respiration.
Nevertheless, when carefully examined, the tropical rainforest soils at L Selva have been
found to have high root, fungal, and bacterial standing crops [26]. Further, organic carbon
may well be an important sink because of the interconnected mycorrhizal plant–fungal–soil
pathways [27]. Therefore, establishing the relative significance of the pathways of carbon
flow is an important step (Figure 4).
A key element of our sensor studies has been the development of a soil monitoring
system installed near the base of the eddy covariance towers. The system consists of
three instrumented soil profiles, each with sensors for soil CO2 and O2 , soil temperature,
and soil moisture at four depths (surface, 5–10, 15–20, 50 cm) totaling 12 sets of sensors.
Additional surface sensors for the soil temperature and moisture were placed to generate
Sensors 2023, 23, 9081 7 of 16

spatial information about the surface soil conditions and select the representative areas for
long-term monitoring. The sensor profiles provide data on the soil dynamics at a level of
detail not typically present at most flux tower sites. In our measurements to date, we have
found that soil respiration is a major component of the ecosystem carbon flux, which is
estimated to comprise approx. half of the total ecosystem respiration. As the new eddy
covariance towers become operational, the soil flux data will serve as an important check
on the carbon flux budget.
The CO2 sensors consisted of a remote Vaisala probe (GMT220 transmitter and GMP221
probe, 0–10% CO2 range) and the O2 sensors (Apogee model SO-110). The sensors were
installed inside a sealed top of polyvinyl chloride (PVC) tubing and exposed end sealed
with a GORE-TEX lining located at the appropriate depth. The temperature and moisture
readings were undertaken using Campbell Scientific CS650 sensors (Logan, UT, USA). All
the sensors were connected to the same data logger for synchronized data. The readings
were recorded at 5-min intervals and could be analyzed independently or averaged using
24-h analyses.
A challenging goal for soil ecosystem research has been the quantification of root
and microbial dynamics and coupling those measurements with sensor data for the soil
temperature, water content, and CO2 and O2 . Our future intent is to collect quantitative
sufficient data to model the CO2 flux using HYDRUS or other existing models to utilize our
soil sensor data (Figure 5). Our initial studies of soil CO2 fluxes have been made within
Sensors 2023, 23, xthe
FORfootprint of the past eddy covariance estimates [12] to better understand how soil CO2
PEER REVIEW 8 of
behaves in this ecosystem [28,29].

Figure 4. Observatory
Figure 4. Soil Ecosystem Soil Ecosystem at Observatory
the La Selva.atThethe white
La Selva.
boxThe white
holds box holds data
a Campbell a Campbell
logger data logg
for recording the sensor data inputs at 5 min intervals. Attached to the data logger are the wirin
for recording the sensor data inputs at 5 min intervals. Attached to the data logger are the wiring
routed through PVC tubes into the soil with buried sensors to measure the temperature an
routed through PVC tubes(Campbell
moisture into the soil with buried
Scientific, Logan,sensors
Utah),to
CO measure the temperature and moisture
2 (Vaisala, Helsinki, Finland), and O2 at four depth
(Campbell Scientific, Logan,
2, 8, 16, Utah),
and 50 CO2details
cm (see (Vaisala, Helsinki,
in text Finland),
[29]). The andhouses
black box O2 at four depths,
the PC 2, 8, 16, the imag
for recording
from the
and 50 cm (see details automated
in text minirhizotron
[29]). The (AMR).the
black box houses ThePCcable
for runs from the
recording the computer to the
images from theAMR with
the PVC tube
automated minirhizotron at a The
(AMR). 45° angle
cable and
runsafrom
meterthe
in computer
length (70 to
cmthedepth).
AMR within the PVC tube
at a 45◦ angle and a meter in length (70 cm depth).
 for recording the sensor data inputs at 5 min intervals. Attached to the data logger are the wiring
routed through PVC tubes into the soil with buried sensors to measure the temperature and
moisture (Campbell Scientific, Logan, Utah), CO2 (Vaisala, Helsinki, Finland), and O2 at four depths,
2, 8, 16, and 50 cm (see details in text [29]). The black box houses the PC for recording the images
Sensors 2023, 23,from
9081 the automated minirhizotron (AMR). The cable runs from the computer to the AMR within 8 of 16
the PVC tube at a 45° angle and a meter in length (70 cm depth).

Figure 5. Carbon cycling

Figure model
5. Carbon showing
cycling modelthe carbon
showing theinputs and outputs
carbon inputs to the
and outputs atmosphere
to the atmosphere and
and soil.
soil.
The reported soil respiration values were low at La Selva, suggesting that we still have
a poor understanding of the processes that regulate soil carbon dynamics in this ecosystem
(Figure 4). The efflux values measured at La Selva were in the range of 3 to 4 µmol m−2 s−1 [28]
in our studies. However, previous studies at La Selva have reported low rates of soil CO2
production of only 1 to 5 µmol m−2 s−1 [28]. In a seasonal dry tropical forest, we identified
soil respiration (Rs) rates of 7 to 8 µmol m−2 s−1 , and our tropical forest measurements found
soil respiration rates as high as 13 µmol m−2 s−1 [29].
We used a gradient-flux method based on the concentrations of CO2 in the soil profile
to estimate soil respiration (Rs) (Figure 4). In a soil context, Rs includes both the CO2 pro-
duction through metabolism and the physical movement of the CO2 molecule through soil
to the atmosphere. The flux-gradient Rs technology has been demonstrated using several
validation applications [30]. We identified the differences in the soil CO2 concentrations
after applying temperature and pressure corrections at multiple depths and computing the
flux based on diffusion kinetics and a gas diffusivity model based on Fick’s first law for
calculating the soil CO2 efflux. We compared the modeled fluxes to the manual measure-
ments using above-ground chambers. This approach was complicated by the derived soil
physical properties, which varied greatly across La Selva and impacted the model results.
Other parameters were found to be helpful in describing the soil processes. We used
CO2 production (Ps) to represent the metabolic production of CO2 , and Rs for soil ecosystem
respiration. Once the concentrations at the different soil layers were known, we calculated
the Ps as the inverse of the differential between the Rs values of the two layers divided by
the depth. Rs integrated both the Ps and diffusion.
Biochemically derived CO2 comes from three primary sources: (a) autotrophic root
respiration (Rr) coming from fixed CO2 ; (b) autotrophic, newly fixed CO2 that is respired
from symbiotic microorganisms, in particular from mycorrhizal fungi (Rmf); and (c) het-
erotrophic CO2 resulting from decomposing organisms (Rh) (Figure 5). To understand the
Sensors 2023, 23, 9081 9 of 16

differing components, and because soil temperature in the humid tropics varies minimally,
we contrasted the overall CO2 production with its components, Rr, Rmf, and Rh.
A key variable for modeling the soil efflux is the amount of air-filled soil pore space (θ),
which is highly variable in time (wet and dry periods) and space (soil texture differences,
canopy interception, microtopography), even at the experimental plot scale. The second is
the tortuous particulate barriers blocking the pathway for gas molecules. The high clay con-
tent of the La Selva soils and high rainfall results in a water layer or extremely high surface
water content, which restricts gas diffusion. We know little about the possible allocation of
carbon to soil and its unavailability for allocation to root and microbe productivity. Is there
a significant loss of carbon to CH4 ? Or is soil CO2 lost by dissolving the soil in water [31]
and moving it out of the system by another pathway? (Figure 5). These possibilities are
intriguing but challenging to address directly.
Automated minirhizotron systems (AMR) were installed adjacent to the soil sensor arrays
and minirhizotrons were installed in order to image the growth of roots and mycorrhizae at
rates set by the user (Figure 6). Our design utilized a Pro-Scope mounted on a sled, which
moved the camera within a glass tube. The camera was connected to a computer and a
120-volt power source with a hot-wired connection for on-site image storage and wireless
transfer. Each image was taken at 100×, creating an image of 3.01 mm × 2.26 mm with an
average depth of field of 0.125 mm (Figure 5), and was stitched into a mosaic using RootView
https://rhizosystems.com/automated-mini-rhizotron/, (accessed on 12 February 2022). The
roots, fungal hyphae, soil particles, and soil invertebrates were identified and measured from
the images. From these images, the roots were distinguished and the root length and standing
crop
Sensors 2023, 23, x FOR from
PEER the root volume was quantified using Rootview, specifically the image recognition
REVIEW 10 of 17
as described https://rhizosystems.com/image-analysis/, (accessed on 12 February 2022).

Figure
Figure 6. Image from6.the
Image from the automated
automated minirhizotron
minirhizotron system showing
system (AMR) (AMR) showing a suberizing
a suberizing fine root,
fine root,
soil aggregates, and arbuscular mycorrhizal fungal hyphal networks.
soil aggregates, and arbuscular mycorrhizal fungal hyphal networks.
Extramatrical AM fungal hyphal lengths were found to be tightly coupled to
Extramatrical AM fungal hyphal lengths were found to be tightly coupled to temper-
temperature and moisture. Therefore, this study used the data from randomly chosen
ature and moisture. Therefore, this study used the data from randomly chosen images
images from the 2010–2012 dataset to create a linear multiple regression model of the daily
from the 2010–2012 dataset to create a linear multiple regression model of the daily root
root respiration. The standing crop AM fungal mass (Rr) was estimated using the standing
respiration. The standing crop AM
crop root biomass valuesfungal
of anmass (Rr)
analog was estimated
species. using
The biomass the standing
estimates for AMcrop
fungal
root biomasshyphae
valueswere
of andetermined
analog species. The biomass estimates for AM fungal hyphae
from the length and diameter measurements and the biomass
carbon determined by [32].
Our soil flux investigations established that there are CO2 pathways within tropical
forest soils that remain poorly understood. One of these is a significant loss of carbon via
dissolved inorganic carbon flowing into streams through impacts from animal activities,
as described below for leaf-cutter ants. The root and AM fungal hyphal production and
Sensors 2023, 23, 9081 10 of 16

were determined from the length and diameter measurements and the biomass carbon
determined by [32].
Our soil flux investigations established that there are CO2 pathways within tropical
forest soils that remain poorly understood. One of these is a significant loss of carbon via
dissolved inorganic carbon flowing into streams through impacts from animal activities,
as described below for leaf-cutter ants. The root and AM fungal hyphal production and
turnover increased below the ant nest footprints [33] and the nest vents created a chimney
venting CO2 that accumulated in soil pipes created by roots [34] and fungal hypha into
nests and out nest openings [34]. A second flux, which remains poorly understood, is
carbon sequestration into glomalin and other organic compounds from roots, mycorrhizal
fungi, and decomposed microbes. We know little about the amount of glomalin production
per unit of fungal hyphal length, and a better accounting of the turnover dynamics will
further our understanding of carbon sequestration in these tropical ecosystems.

6. Impacts of Leaf-Cutter Ants on Biogeochemical Cycles

Leaf-cutter ants are geographically widespread and abundant in lowland neotropical
forests where they are “ecosystem engineers” with a significant effect on the ecosystem
processes of carbon and nitrogen cycling (Figure 7). They account for as much as one
Sensors 2023, 23, x FOR PEER REVIEW
quarter of all herbivores in these forests, and their symbionts may be responsible for 11
significant heterogeneity in soil nitrogen resources (Figure 5). Through their herbivory, leaf-
cutter ants change their environment by creating canopy gaps, transferring organic matter
underground, enhancing
matter soil aeration
underground, and turnover
enhancing rates, and
soil aeration and increasing soil nutrient
turnover rates, and increasing
availability and nitrogen fixation [35–38].
nutrient availability and nitrogen fixation [35,36,37,38].

Figure
Figure 7. Image from7.the
Image from the
automated automated minirhizotron
minirhizotron (AMR) system(AMR) system
showing showingfine
a suberizing a suberizing
root, fine
soil aggregates, and arbuscular mycorrhizal fungal hyphal networks. Photo by Carlos de la Ro
soil aggregates, and arbuscular mycorrhizal fungal hyphal networks. Photo by Carlos de la Rosa.

Leaf-cutter
Leaf-cutter ants transportants transportamounts
substantial substantial amounts
of organic of organic
material into material into
their nests their nests
and
increase
increase the soil the matter
organic soil organic matter
pool that pool
fungi that
and fungi and
bacteria bacteria
transform transform
into gaseousinto
and gaseous
aqueous
aqueous phases. phases.
Their Their nests
nests appear appear of
as mounds asexcavated
mounds ofsoil excavated
marked soil marked by nume
by numerous
entrances andentrances
gas ventsand
thatgas
leadvents that
to an lead tonetwork
intricate an intricate network
of tunnels andof chambers.
tunnels and chambers. U
Using
the plant material they collect, leaf-cutter ants cultivate an obligate
the plant material they collect, leaf-cutter ants cultivate an obligate symbiotic fungus, whichsymbiotic fun
which they consume as food. Modifying the biotic and abiotic components in t
habitats and regulating the availability of resources, they influence other species.
The combined concentration of plant material with fungal and ant activity is h
This activity makes leaf-cutter nests hot spots for biogeochemical cycling [39,40]. T
Sensors 2023, 23, 9081 11 of 16

they consume as food. Modifying the biotic and abiotic components in their habitats and
regulating the availability of resources, they influence other species.
The combined concentration of plant material with fungal and ant activity is high.
This activity makes leaf-cutter nests hot spots for biogeochemical cycling [39,40]. Their
nests alter the physical and chemical properties of soils, and the fungus gardens inside the
nests are sites of symbiotic N2 fixation [38]. The roots and fungal hyphae preferentially
grow inside the nests and their turnover contributes to the soil carbon pool. All these
processes directly fertilize the nest soils and hypothetically promote CO2 efflux. As forests
become increasingly fragmented across the Neotropics because of land use changes due to
agriculture and grazing, leaf-cutter ants are becoming more abundant [37,40,41] and their
impact on soil carbon dynamics is expected to increase.
Our research investigated the carbon dynamics as influenced by leaf-cutter ants and
their nests and differentiated the sources of CO2 efflux between the activities of ants, fungi,
the nest microbial community, and roots and hyphae (Figure 8). Additionally, we quantified
the nitrogen and phosphorus biogeochemistry of ant nests to determine their legacy effects
after the nests are abandoned. This research involved a multifaceted approach using new
Sensors 2023, 23, x FOR PEER REVIEW 12 of 17
technologies to couple continuous measurements of the soil CO2 with discrete measures of
13
the CH4 efflux, as well as the isotopic δ C composition, soil carbon pools and fluxes, soil
nutrient concentrations, estimates of root and fungal dynamics, and microbial community
nests,
and paired control
functional sites,
indices. Theand along a chronosequence
measurements of out
were carried abandoned nests paired
on ant nests, to quantify the
control
legacy
sites, effects.
and along a chronosequence of abandoned nests to quantify the legacy effects.

Figure 8.
Figure 8. Diagram
Diagram of
of aa leaf-cutter
leaf-cutter ant
ant (Atta
(Atta cephalotes)
cephalotes) nest
nest comprised
comprised ofof interconnected
interconnected fungal
fungal and
and
refuse chambers.
refuse chambers. The
The arrows
arrows depict
depict the
the CO
CO22 fluxes
fluxes between
between the
the nest
nest structures,
structures, surrounding
surrounding soil,
soil,
and atmosphere.
and atmosphere. The
The sensor
sensor network
network components
components monitor:
monitor: (A)
(A) the
the soil
soil moisture,
moisture, temperature,
temperature, and
and
CO2 concentration at multiple depths; (B) CO2 emissions from nest tunnel openings; and (C) the CO2
CO2 concentration at multiple depths; (B) CO2 emissions from nest tunnel openings; and (C) the CO2
efflux from the soil (see text for details).
efflux from the soil (see text for details).

The CO
The COconcentrations
2 concentrations in nest tunnels were higher than the background
in nest tunnels were higher than the background (atmospheric)
2
(atmospheric)
levels levelsexceeded
and at times and at times exceeded
5% (by volume)5% in(bythe
volume) in the ventstoconnected
vents connected the fungaltoand
the
fungal and refuse chambers [42,43,44]. Thus, the nest soils adjacent to these
refuse chambers [42–44]. Thus, the nest soils adjacent to these tunnels were nutrient hot tunnels were
nutrient
spots, hot spots,
emitting moreemitting
CO2 thanmoretheCO 2 than the soils away from the nests. By continuously
soils away from the nests. By continuously excavating
excavating the ventilation network in their nests,
the ventilation network in their nests, leaf-cutter leaf-cutter
ant colonies ant adequate
maintain colonies CO maintain
2 and
adequate CO 2 and O 2 concentrations (Figure 8). Prior to our research,
O2 concentrations (Figure 8). Prior to our research, the CO2 emission rates had not the CO 2 emission
been
ratescharacterized,
well had not been and wellthe
characterized, and the potential
potential connection between theconnection between
nest air and the nest air
the surrounding
and soils
nest the surrounding
had not been nest soils had
recognized not been
(Figure 8). Therecognized (Figure
CO2 emissions 8).the
from The CO
soil 2 emissions
matrix to the
from the soil matrix to the nest air can be significant if the opposite gradient occurs and
the air in the nest has a lower CO2 concentration than the surrounding soil. This situation
can establish a significant ventilation pathway, given the large surface of the nest walls
and tunnels. An accurate characterization of the nest and nest soil emissions has improved
our understanding of the role of leaf-cutter ants in carbon cycling in tropical forest
Sensors 2023, 23, 9081 12 of 16

nest air can be significant if the opposite gradient occurs and the air in the nest has a lower
CO2 concentration than the surrounding soil. This situation can establish a significant
ventilation pathway, given the large surface of the nest walls and tunnels. An accurate
characterization of the nest and nest soil emissions has improved our understanding of the
role of leaf-cutter ants in carbon cycling in tropical forest ecosystems.
The traditional methods for measuring soil carbon emissions would easily overlook
CO2 fluxes contributions from ant nests, but this blind spot could cause scientists to miss out
on important emission sources. We found delicately balanced ventilation networks which
leverage the gas density difference (free convection) to expel elevated CO2 concentrations
from these large subterranean networks of tunnels, fungal gardens, and debris chambers
nests [35]. At night, we observed that when the above-ground air temperature drops, warm
and less dense nest air rises out of the nest. We estimated the CO2 emissions from the
tunnels using CO2 sensors held over the tunnel mouths by small acrylic cylinders. The
vents themselves emitted much more carbon dioxide than the soil. The measurements
of the gas flowing out of individual vents showed that carbon dioxide emissions were
10,000 to 100,000 times greater than the values measured from the soil, although the vent
emissions only represented a small fraction of the total emissions from the rainforest. In
addition, the leaf-cutter ants themselves often responded to our disturbances by directing
workers to the area to excavate new tunnels around the edges of the cylinders.

7. Evolving Sensor Modalities

The technologies developed for sensors to measure the temporal and spatial scales of
our physical environment are generally more mature and robust in design than the existing
technologies for chemical or biological sensors. A large commercial base exists for the
design and manufacture of diverse modes of sensors for temperature, pressure, and physical
properties (Table 1). Expanding on these existing commercial sensors, there is a need for
modular sensor arrays and data loggers to provide three-dimensional parametric data for
air, water, soil, and groundwater over spatial scales ranging from the micro (e.g., pore
volume) to the mega (e.g., kilometer scale volumes). Innovative new imaging techniques
for physical parameters are now available to assist in mapping the biogeochemical fluxes in
spatial volumes at diverse scales. Multiple devices are now available to map atmospheric
turbulence using 3D flow measurements at fine scales of a few cm.
There is a clear need for an innovative development of chemical sensors for use in a
variety of natural and anthropogenic environments (e.g., atmospheric, terrestrial (soils and
sediments), and aquatic (groundwater, fresh and marine waters). Many existing chemical
sensors are not robust enough to measure the key or fundamental chemical compounds and
ions in sustained operations at high acquisition rates. Moreover, there is a need for greater
precision and sensitivity to expand flux measurements at dynamic spatial and temporal
scales (Table 1). Many electrochemical and optical oxygen sensors are known to be prone
to biofouling for short periods of time. Biological sensors would be useful to measure
diverse biological reactions. Oxygen, basic nutrients, hydrogen sulfide, pH, CO2 , NOx,
SOx, CH4 , CO, O3 , Fe, Mn, and trace metals all may have significance in the ecosystem
studies of biogeochemical fluxes and dynamics. As with the other types of sensors, the
signals produced by biological sensors need to be processed in ways that allow for adaptive
sensing. Furthermore, the sensors need to be capable of long-term deployment, and should
be capable of integration with other sensing devices.
Sensors 2023, 23, 9081 13 of 16

Table 1. Examples of major sensor modalities with comments on cost, reliability and power requirements.

Category Example Comments

Temperature (e.g., thermocouples,
Physical Inexpensive to intermediate cost, reliable, low powerequirements
thermistors, IR sensors)
Relative humidity Intermediate, reliable, low power
Leaf wetness Intermediate, reliable, low power
Inexpensive to moderate, issues with calibration, low power,
Soil moisture
manchoices
PFD, total irradiance Intermediate, reliable with calibration issues, low power
Wind speed and direction
Inexpensive to intermediate, reliable, fail at low wind speed, low
cup anemometer
power
hot wire anemometer Intermediate, less reliable, high power
2-D/3D sonic anemometer Intermediate to expensive, very reliable, moderate power
Chemical Atmospheric CO2 Expensive, moderate power, requires careful calibration
Soil CO2 Intermediate, reliable low power, requires careful calibration
Soil CO2 efflux Expensive, reliable, moderate power. Requires careful calibration
Nitrate sensor Expensive, under development for field use
Phosphorus sensor Not available for field use
Moderately expensive, reliable, moderate power, high band width,
Biological Digital imagers
software issues
Minirhizotron camera Expensive, variable power requirements
Sap flow sensors Moderate cost, reliable, calibration issues
Acoustic sensors Moderate, reliable, high band width, software issues

There is great promise in the future development and installation of new sensor networks
to involve new sensor modalities and expand traditional sensors for microclimate (Table 1).
These include imagers and acoustic monitoring devices as sensors for detecting motion, vo-
calization, and other organismal activities and behaviors. There are, nevertheless, numerous
challenges in designing and deploying successful ecological sensor networks. Some of these
issues relate to science-driven questions and requirements that are specific to terrestrial, soil, or
aquatic domains. In an observatory mode of operation, the goal is to provide a more complete
“fingerprint” of ecosystem structure and function over time and space.
Micrometeorologists have been measuring the CO2 and water vapor exchange between
vegetation and the atmosphere since the late 1950s and early 1960s. However, the routine
application of the eddy covariance methodologies and associated data management that
allowed for continuous flux measurements did not occur until the 1980s. Technological
advances were made at this time in sonic anemometry, infrared spectrometry, and digital
computation. Further technological developments over the past several decades have
facilitated a larger data storage capacity, and the improved stability and precision in
instruments have enabled scientists to build on pioneering ecosystem flux studies. Today,
AI (artificial intelligence) is opening the door to new ways of monitoring the pulse of our
environment and addressing the issues of global change.

8. Challenges of Working with Sensors in a Humid Tropical Rainforest and

Lessons Learned
As with any technology, there are limitations and challenges to working at La Selva
with a warm and humid environment that is characteristic of tropical rainforest ecosystems.
In our experience, we had to learn to anticipate practical problems when working with
limited access to spare parts by developing procedures to maximize the life of the sensors
and sensor arrays. Moreover, numerous modifications were necessary to successfully
operate our sensor arrays under the extreme conditions of high temperatures and humidity,
torrential periods of rainfall, and flooding. For example, rust and microbial growth in the
humid environment requires high-quality stainless metal parts and care in the use of plastic
tubing, which can be readily and quickly overgrown with fungal hyphae. The need to
Sensors 2023, 23, 9081 14 of 16

thoroughly seal all openings, holes, or gaps in sensor housings and instrumentation was
also critically important to prevent insect colonization. We quickly learned that almost
any exposed metal surface or opening on the sensors and instruments will rust, promote
fungal growth, and/or be colonized by ants or other insects. Consistent AC power was
generally not a problem, but power surges and brief outages are to be expected in remote
field stations. AC-powered elements must be outfitted with surge protectors. Our only
experience with an extended power loss at the towers occurred when thieves pulled and
stole the 1 km of copper wire that linked the towers to the La Selva laboratory.
An additional challenge of working in tropical rainforest ecosystems like La Selva
is the presence of ferocious stinging ants and venomous fer-de-lance snakes. A focus on
these biological hazards was a concern taken very seriously by the engineers in our group,
which limited their field activities in the forest. However, we noted that the biologists in
our group were much less affected.
The three original towers forming the La Selva Canopy Tower Network were erected
in 2008. Since the La Selva environment had a history of strong storms with high winds
and lightning, we took care to take all manner of precautions to protect the towers. The
towers were carefully grounded with heavy copper cable to protect them against lightning.
Intellectually, we knew that the median lifespan for tropical forest trees was about 120 years.
However, we failed to appreciate that it meant that one out of 100 trees rooted close to the
towers could be expected to fall each year. We were careful to cable the trees positioned
near the towers to reduce potential damage from treefalls. Guywires stabilized the towers
and were attached with breakaway bolts to keep the towers from being pulled down if a
tree or branch were to fall on the wires.
Within six months, we had a major lightning strike to the tower that destroyed much of
the instrumentation on one of the towers despite its grounding. In December 2008 and again
in March 2009, we had a large tree branch fall against the guywires and damage parts of the
towers, despite the special bolts, and detached the towers from their foundations. While
none of the research instrumentation was seriously damaged, several projects and their
data streams were interrupted, and the availability of space for projects was substantially
reduced. In the following years, we experienced a large branch fall in June 2012, which
seriously damaged the instrument room at the base of the towers. A treefall hit one of the
towers in September 2013, and another in September 2015 knocked two towers off their
foundations and pulled down the canopy walkway. A tornado in May 2018 blew down
two of the towers and another tree fell against a tower. Most recently, a large falling tree in
October 2021 destroyed one of the towers.
Through all of this, the La Selva Canopy Tower Network has prevailed and continues
to provide valuable data and instrumentation for a variety of research projects. We hope
that the lessons we have learned will be of value to others.

Author Contributions: P.W.R., T.C.H., A.S.F.-B. and M.F.A. jointly conceived and designed the
research protocols. P.W.R. wrote the first draft of the manuscript and all authors reviewed the text
and made edits. All authors have read and agreed to the published version of the manuscript.
Funding: This research was supported by the U.S. National Science Foundation under the grants
ANI-00331481 and CCR-0120778.
Institutional Review Board Statement: This study did not involve humans or animals.
Informed Consent Statement: This study did not involve humans.
Data Availability Statement: Data are contained within the article.
Acknowledgments: We gratefully acknowledge the help of the staff members from the La Selva
Biological Research Station who provided critical assistance and permits to make this research
possible, and especially to Orlando Vargas and Enrique Castro who kept the towers working. Many
others in our research groups contributed significantly to our program of ecological research on
ecosystem fluxes at La Selva.
Sensors 2023, 23, 9081 15 of 16

Conflicts of Interest: The authors declare no conflict of interest. There were no sponsors that had a
role in the design of the study; in the collection, analyses, or interpretation of the data; in the writing
of the manuscript; or in the decision to publish the results.

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