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Controlling Humidity Above Ambient with the CIRAS-3 Portable Photosynthesis System

Often, the desired environment for photosynthesis measurements is for the leaf cuvette to be controlled to ambient humidity conditions outside the cuvette. If instead, it is desired to have the leaf cuvette humidity above ambient, it can be accomplished easily and safely by adding moisture-holding foam around the equilibrator element on the outside of the CIRAS-3 enclosure as shown below.

A humidity equilibrator is part of the Air Supply absorber assembly. Its normal function is to bring the gas stream back to ambient humidity after passing through the sodalime CO2 absorber column which always adds humidity to the ambient gas as it removes CO2. By surrounding the equilibrator with saturated foam, paper towels, or even a kitchen sponge, the gas can be brought close to the saturation vapor pressure. Then, any of the CIRAS-3 control modes will work to control the humidity to any desired level.

Elevated humidity condition with equilipbrator in saturated foam in same dry ambient condition

The drawing to the right this shows the size of two foam inserts that can be installed into the absorber assembly and surround the equilibrator Nafion tubing. Liquid water can be added to the top of the equilibrator while the CIRAS-3 is in operation and running. There is no danger of getting liquid water into the CIRAS-3 internals due to the function of the Nafion tubing. Excess water can harmlessly drip out the bottom of the absorber assembly without concern. Note: The PDF to the right contains the template at actual size when the PDF printing option “Actual Size” is chosen.

Foam Inserts Assembly into Absorber
Foam Inserts Assembly into Absorber.
Foam Inserts Assembly into Absorber 2
Where to add water as needed.
Controlling Humidity Above Ambient - CIRAS-3
Foam Inserts for Absorber mm[in].
Print actual size template from the PDF below.
Be sure to print PDF at “Actual Size”.

Material: Aquazone Foam1/4 inch thick – McMaster-Carr 8884K41 or equivalent. Alternate Material: any water absorbing foam or kitchen sponge.

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Measuring Soil CO2 Efflux from Ant Nests in the Brazilian Rainforest

A common assertion is that tropical forests (especially tropical wet forests) are more productive than temperate forests, and on an annual basis, rates of net primary productivity (NPP: carbon fixed per unit area per year) of tropical wet forests greatly exceed rates of NPP in temperate deciduous or coniferous forests. Yet, on shorter time scales (daily or monthly), NPP of temperate forests is about equal to that of NPP of tropical forests, and “ecologically relevant” productivity is thought to be highest in latitudes between 30° and 50° [1]. Comparable data for organisms at other trophic levels, however, are scant; for example, the carbon flux rate from soils (i.e., “soil respiration”) is a crucial part of any terrestrial ecosystem model, but values for soil respiration used in ecosystem models include only soil microbes and plant roots. Although soil respiration of ant nests rarely has been measured in the field [2], nests of red wood ants (Formica rufa group) in northern Europe have respiration rates nearly five times higher than that of surrounding ant-free soils [3]. How this compares to tropical ants is unknown, but extrapolation from temperate studies suggests that contribution of ants to carbon cycling in tropical ecosystems could be quite large.

With support from the Museo Paraense Emílio Goelde in Belém, Brazil, Drs. Aaron M. Ellison (Harvard University, Harvard Forest) and Rogério R. Silva did a pilot study of CO2 efflux from ant nests at the Caxiuanã National Forest, Pará, Brazil. Instantaneous rates of soil carbon efflux from nests of five species of ground-nesting and arboreal-nesting ants and nearby soils lacking ants were measured for COwith an EGM-5 Portable CO2 Gas Analyzer and an SRC-2 Soil Respiration Chamber.

CO2 efflux rates from ant-free soils (mean = 1.3 µmol CO2 m-2 s-1) and from nests of the ground-nesting Mycoperus and Pheidole spp. were lower than those measured previously during the dry season at Caxiuanã (≈3 µmol CO2 m-2 s-1) [4], but efflux rates of both leaf-cutter ants (Atta sp.) and fire ants (Solenopsis sp.) were substantially higher than background (ant-free) levels. CO2 efflux from nests of the arboreal nesting Odontomachus species also were comparable to ant-free soils. Future work will include more extensive measurements of these and other ant species, adjacent ant-free soils, and large arboreal nests of Azteca species. Together, these data will help to improve estimates of soil CO2 fluxes from tropical forests.


[1] Huston, M. A., and S. Wolverton. 2009. The global distribution of net primary production: resolving the paradox. Ecological Monographs 79: 343-377.

[2] Peakin, G. J., and G. Josens. 1978. Respiration and energy flow. Pages 111-163 in M. V. Brian, editor. Production Ecology of Ants and Termites. Cambridge University Press.

[3] Jílková, V., T. Cajthaml, and J. Frouz. 2015. Respiration in wood ant (Formica aquilonia) nests as affected by altitudinal and seasonal changes in temperature. Soil Biology and Biochemistry 86: 50-57.

[4] Sotta, E. D., E. Veldkamp, B. R. Guimarães, R. K. Paixão, M. L. P. Ruivo, and S. S. Almeida. 2006. Landscape and climatic controls on spatial and temporal variation in soil CO2 efflux in an Eastern Amazonian rainforest, Caxiuanã, Brazil. Forest Ecology and Management 237: 57-64.

PP Systems would like to thank and acknowledge Aaron M. Ellison, (Harvard University, Harvard Forest, Petersham MA, USA) for providing the information contained in this application note.

If you would like to learn more about this exciting research, please contact PP Systems.

Follow Aaron M. Ellison: The unBalanced ecoLOGist

EGM-5 SRC-2 Soil CO2 Flux
Figure. Estimates of CO2 efflux from ant nests at Caxiuanã and ant-free soils (“0 Control”). Box plots illustrate medians, quartiles, and upper and lower deciles; widths of the boxes are proportional to sample size, and points denote values of individual observations taken in the morning (red), mid-day (green), and afternoon (blue).
EGM-5 Portable CO2 Gas Analyzer and SRC-2 Soil Respiration Chamber on a Solenopsis nest at the Caxiuanã field station.
Custom collar on a Mycocepurus nest in the lab compound at the Caxiuanã field station.
Aaron Ellison (left) and Rogério Silva (right) measuring CO2 efflux from a Solenopsis nest at Caxiuanã.

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Studying Volcanic Activity Using Drones and Sensors to Accurately and Precisely Predict Volcanic Explosive Eruptions

A team of research scientists from McGill University (Montreal, Quebec CANADA), Universidad de Costa Rica (San Jose, Costa Rica), and the Observatorio Vulcanológico y Sismológico de Costa Rica (Heredia, Costa Rica) are currently developing a series of drones and associated instrumentation to study Turrialba volcano in Costa Rica. This volcano has shown increasing activity during the last 20 years, and the volcano is currently in a state of heightened unrest as exemplified by recent explosive activity in May-August 2016. The eruptive activity has made the summit area inaccessible to normal gas monitoring activities, prompting development of new techniques to measure gas compositions. The team has been using two drones, a DJI Spreading Wings S1000 octocopter and a Turbo Ace Matrix-i quadcopter, to airlift a series of instruments to measure volcanic gases in the plume of the volcano.

These instruments comprise optical and electrochemical sensors to measure CO2 (SBA-5 CO2 Gas Analyzer – PP Systems), SO2, and H2S concentrations which are considered the most significant species to help forecast explosive eruptions and determine the relative proportions of magmatic and hydrothermal components in the volcanic gas. The integrated payloads weigh 1-2 kg, which can typically be flown by the drones in 10-20 minutes at altitudes of 2000-4000 meters. Our broader goals are to map gases in detail with the drones in order to make flux measurements.

MINIGAS – Developed at the Universidad de Costa Rica, this compact instrument measures CO2, SO2, and H2S , as well as GPS location, pressure, temperature, and humidity. Data are stored on data loggers and can also be transmitted by telemetry. Total weight is 1.2 kg.

MICROGAS – Developed at McGill University, this instrument measures CO2, H2O, SO2, and H2S. The CO2-H2O infrared sensor is made by PP Systems, while the SO2 and H2S electrochemical sensors are made by City Technology. Data are recorded on Grant Yoyo dataloggers. The entire package including battery weighs 1.14 kilograms.

We now have the means to forecast explosive eruptions. The key information that is gathered includes gas, seismic, and geodetic data which indicate (a) overpressure and (b) open system behavior. See Examples 1 through 4.


Example 1: From: De Moor et al. 2016, J. Geophys. Res. 121, 5761-5775

Example 2: From: Narváez M. et al. 1997, J. Volcanol. Geotherm. Res. 77, 159-171; Gómez M. and Torres C., 1997, J. Volcanol. Geotherm. Res. 77, 173-193

Example 3: From: Martinelli 1990, J. Volcanol. Geotherm. Res. 41, 297-314

Example 4: From: Druitt et al. 2002, Geol. Soc. London Mem. 21, 281-306

PP Systems would like to thank and acknowledge (left to right) Ernesto Corrales (GAS Lab, CICANM-Univ. de Costa Rica), Fiona D. D’Arcy (McGill University, Montreal, QC Canada), Maarten J. de Moor (Observatorio Vulcanológico y Sismológico de Costa Rica, Heredia, Costa Rica), Dr. John Stix (McGill University, Montreal, QC Canada), Alfredo Alan (GAS Lab, CICANM-Univ. de Costa Rica), and Dr. Jorge Andres Diaz (GAS Lab, CICANM-Univ. de Costa Rica) (not shown) and for providing the information contained in this application note.

Corrales D’Arcy de Moor Stix Alan Diaz

Learn more about McGill University Earth and Planetary Sciences Department Volcanology Research Group here. Follow them on Facebook.

Click here for more information on the SBA-5.  If you would like to learn more about this exciting research, please contact PP Systems.

For application notes on PP Systems’ products, click Application Notes.

SBA-5 CO2 Gas Analyzer including H2O sensor, pump and enclosure.
Example 1. Turrialba 2014-2015 (Costa Rica): CO2/sulfur ratio increases substantially prior to explosive eruptions and ash emissions
PP Systems SBA-5 CO2 Gas Analyzer
Example 2. Galeras 1993 (Colombia): Monochromatic seismic signals (“tornillos”) systematically increase in number and duration, and decrease in dominant frequency, prior to explosive eruptions.
Example 3. Nevado del Ruiz 1985 (Colombia): Banded tremor on 7 September, 4 days prior to ash emission on 11 September. Each tremor cycle is 15-20 minutes’ duration.
Example 4. Soufrière Hills volcano, 1997 (Montserrat): Inflation cycles shown in (a), RSAM in (b). Peaks in tilt and RSAM correspond to vulcanian eruptions. Note the ~12-hour cyclicity from 4 to 9 July.

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Physiology and Vascular Anatomy of Different Avocado Genotypes Relative to Laurel Wilt Susceptibility

Laurel wilt, caused by the fungus Raffaelea lauricola, and carried by bark beetles, is a serious plant disease that has decimated members of the Lauraceae plant family in the southeastern United States since the early 2000s when it was first detected in the US. Originally found infecting forest trees, it was observed in a commercial avocado orchard in Florida in 2012, and now poses a grave threat to Florida’s avocado industry. Infected trees wilt and usually die due to plugging of the vascular system. The disease has spread as far west as Texas and could pose a huge threat to the multi-billion dollar avocado industries of California and Mexico if it spreads to those areas.

Laurel wilt has become such serious concern that a large multi-state, interdisciplinary project, funded by a USDA Specialty Crops Grant is underway to help find a solution to the disease. One of the components of this project being investigated by Drs. Bruce Schaffer and Randy Ploetz, PhD student Raiza Castillo and Biologists Ana Vargas, Josh Konkol, Aime Vazquez, and Randy Fernandez, and collaborator Dr. Ed Etxeberria at the University of Florida, Citrus Research and Education Center, is to determine the relative susceptibility of different avocado races and scion/rootstock combinations in relation to differences in avocado tree physiology and vascular anatomy.

The avocado species, Persea americana, is divided into three botanical races, Mexican (M), Guatemalan (G) and West Indian (WI). In Florida, all commercial avocado scions are grafted on seedling WI cultivars, primarily ‘Waldin’. Commercially available clonal rootstocks (M and G) developed in California and elsewhere, not currently used in Florida, are being tested and compared with clonally propagated material of the seedling WI rootstocks currently used in Florida for their resistance to laurel wilt.

Physiological attributes of different avocado genotypes are being tested to identify tolerance to the laurel wilt. Prior work with commercial cultivars indicated that G and MxG hybrid cultivars were significantly more tolerant to laurel wilt than WI cultivars (Ploetz et al., 2012). The relationship between differences in laurel wilt susceptibility to host physiology among different avocado cultivars was recently investigated (Ploetz et al., 2015; Schaffer et al., 2014). Prior to inoculation, significantly higher xylem sap flow rates were observed in the most susceptible cultivar, ‘Russell’ (WI), but after inoculation sap flow rates were significantly reduced in ‘Russell’ relative to ‘Marcus Pumpkin’ (G) or ‘Brogdon’ (MxGxWI hybrid). Net CO2 assimilation (A), stomatal conductance of H2O (gs) and transpiration (E) determined CIRAS-2 and CIRAS-3 portable gas exchange systems have been determined to be excellent non-destructive measures for disease-induced stress (Ploetz et al., 2013; Schaffer et al., 2014). Also, scanning electron microscopy is being used to assess xylem anatomy as it relates to tree physiology and disease susceptibility in avocado genotypes being evaluated.

The impacts of clonal rootstocks and root/stock scion combinations of different botanical races of avocado on the development of laurel wilts disease and the relationship between disease development and the xylem physiology and anatomy are being evaluated. From these studies, Information is being obtained about the relative susceptibility of different avocado races and influence of physiological variables on relative to disease susceptibility. This should lead to the identification of avocado rootstocks and/or the development rootstock/scion combinations that are resistant to laurel wilt disease.


Ploetz, R. C., Pérez-Martínez, J. M., Smith, J. A., Hughes, M. C., Dreaden, T. J., Yu, Y., and Inch, S. 2012. Responses of avocado to laurel wilt, caused by Raffeala lauricola. Plant Pathology 61:801-808.

Ploetz, R.C., Schaffer, B., Vargas, A.I.. Konkol, J.L., Salvatierra, J., Inch, S.A., Campbell, A. and Wideman, R. 2013. Physiological impacts of laurel wilt on avocado. Phytopathology 103(S):114 (abstract).

Ploetz, R.C., B. Schaffer, A.I. Vargas, J.L. Konkol, J. Salvatierra and R. Wideman. 2015. Impact of laurel wilt, caused by Raffaela lauricola, on leaf gas exchange and xylem sap flow of avocado, Persea americana. Phytophathology 105:433-440.

Schaffer, B., Ploetz, R.C., Vargas, A.I., Konkol, J. and Salvatierra, J. 2013. Laurel wilt differentially affects xylem sap flow of three avocado cultivars. HortScience 48:S322 (abstract).

We would like to thank Dr. Bruce Schaffer (University of Florida-TREC) and Dr. Randy Ploetz (University of Florida-TREC) and their graduate students for providing the content contained in this application note.

Click here for more information on the CIRAS-3 Portable Photosynthesis System.

If you would like to learn more about this exciting research, please contact PP Systems.

avocado genotyp laurel wilt
Raiza Castillo (University of Florida – Tropical Research & Education Center – Homestead, FL) performing measurements of leaf gas exchange and chlorophyll fluorescence using the CIRAS-3 Portable Photosynthesis System
Net CO2 assimilation (A) and external severity of laurel wilt on ‘Brogdon,’ ‘Marcus Pumpkin’ and ‘Russell’ avocado trees before (-day) and after (+days) inoculation with Raffaelea lauricola. Different upper case letters indicate significant differences in A among cultivars and different lower case letters indicate significant differences in disease severity among cultivars. From Phytopathology 2015, 105:433-440.

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