SITES_bård 160701-4

2017 > 04

The research station is equipped with all our needs, from field equipment to modern labs and instruments, and is the basis for every day to day work - Gerard Rocher Ros
PhD student Gerard Rocher Ros has described the benefits of teaching intertwined with research at a national research infrastructure.

Read his full blog post here
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What are you doing at the moment?

I am working on my MSc thesis. It is about radiometric calibration of UAV images for vegetation mapping.

My supervisor is Lars Eklundh. I work in collaboration with Per-Ola Olsson, Hongxiao Jin and Stephania Zabala. We are part of the Remote Sensing group at the Department of Physical Geography and Ecosystem Science (INES) in Lund University.
Fig. 1.  Stephania (left) and Ximena (right) with all the equipment, ready to go to the field. Photo by Miguel Castro.
Fig. 1. Stephania (left) and Ximena (right) with all the equipment, ready to go to the field. Photo by Miguel Castro.
Fig 2. The camera calibration starts on the roof of the department. Close pictures of reflective targets and other features, as vegetation, are taken. Right after the picture, the reflectance is measured with the spectrometer. Photo by Ximena Tagle.
Fig 2. The camera calibration starts on the roof of the department. Close pictures of reflective targets and other features, as vegetation, are taken. Right after the picture, the reflectance is measured with the spectrometer. Photo by Ximena Tagle.

What exactly are you doing when calibrating?

I am trying to reduce radiometric issues when processing UAV imagery from a multispectral camera. I chose to work with the Micasense Redge camera. The aim is to obtain quite homogeneous orthomosaics in relation to the light variation. In addition, I am studying the relationship between reflectance values at the ground, and the Digital Numbers (DN) from the camera in order to provide orthomosaics with reflectance values.

For this purpose, on each mission we get data from a downwelling light sensor (DLS) that provides irradiance at the sensor; irradiance measurements from a spectrometer located on the ground; and PAR data from the Eddie covariance tower located at the site. With this data, I am trying to remove light variation among images. After this task, I am performing a normalization of the images (histogram matching).

Regarding the reflectance relationship, I use an ASD spectroradiometer to measure the reflectance of three near Lambertian reflective targets and other features as bare soil, vegetation and water. The reflective targets are used to calibrate the model, and the other features are used for the validation of the model.

Once the images are calibrated, the orthomosaic is produced. Orthomosaics are generated from several images that overlap, using the Structure from Motion (SfM) technique.
Fig. 3. Calibration of the Downwelling Light sensor at Lönnstorp. Per-Ola had to rotate the UAV in different ways according to the Micasense application (connected via WIFi to the cellphone). Photo by Ximena Tagle.
Fig. 3. Calibration of the Downwelling Light sensor at Lönnstorp. Per-Ola had to rotate the UAV in different ways according to the Micasense application (connected via WIFi to the cellphone). Photo by Ximena Tagle.

How should this information be used further on?

The Explorian UAV (the biggest UAV we have now), has a Sony RGB camera, a multispectral camera (Micasense Rededge) and a thermal camera (FLIR). They will be used together to study the influence of spatial heterogeneity and temporal variations of vegetation and land surface on ecosystem carbon fluxes. The idea is to upscale data from the flux towers to a landscape level using spectral indices derived from remotely sensed data. In order to do this, it is recommended to work with homogeneous orthomosaics adjusted with the reflectance values, the tasks I am working with at the moment.
Fig. 4. a) UAV flying over the reflective targets at Lönnstorp. b) Picture of the targets from the UAV. Photo by Ximena Tagle.
Fig. 4. a) UAV flying over the reflective targets at Lönnstorp. b) Picture of the targets from the UAV. Photo by Ximena Tagle.

Tell us about yourself!

I am Ximena Tagle. I work at the Research Institute of the Peruvian Amazon, at the program of Forest management and environmental services. I am doing my MSc thesis to obtain a degree in Geo-information Science and Earth Observation for Environmental Modelling and Management (GEM).
Fig. 5. (Me) connecting the spectrometer for its calibration with the spectralon (white circle in the picture) before the measurements. Behind it can be seen the Explorian UAV. Photo by Miguel Castro.
Fig. 5. (Me) connecting the spectrometer for its calibration with the spectralon (white circle in the picture) before the measurements. Behind it can be seen the Explorian UAV. Photo by Miguel Castro.

Finally, anything more to add?

This task is very interesting because it is a new topic, so we are having challenges most of the time. We have to be creative to solve different issues. We have to be persistent as well. I find inspiration when we attend conferences or workshops, and there are people who are studying similar issues and we can discuss new solutions; we are learning all the time! This field is developing so fast that you must try to keep track of the innovations.
Fig. 6. The Explorian 8 UAV. Photo by Ximena Tagle.
Fig. 6. The Explorian 8 UAV. Photo by Ximena Tagle.

Thanks for this insight Ximena and SITES wish you good luck with the MSc thesis!

Stephania Zabala and Ximena Tagles MSc projects are part of the integrating facility SITES Spectral.

Both Ximena and Stephanias MSc Projects are part of the EU Erasmus program in Environmental Modelling and Management (GEM).
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Grimsö is unique as a centre for wildlife ecology studies in Sweden. Results from the annual and long-term monitoring of wildlife species are transferred to knowledge and used in research and natural resource management. SITES have spoken to three key persons and asked them about the environmental monitoring, inventories and research about small rodents. Let’s meet, Gunnar Jansson, Frauke Ecke and Petter Kjellander.

Two times every year Grimsö set up and perform the small rodent survey, in May and September. This monitoring series is one of nineteen at Grimsö, where the others focus e.g. moose, fox and starling. This year, 2017, is the 45th year in a row with this small rodent survey, which includes voles, mice and shrews. The larger rodents, beaver, hare and rabbit are not included in this inventory.

Gunnar Jansson is a researcher and coordinates SITES operations at Grimsö. He explains that the purpose of the inventories is to follow the population dynamics of the small rodents, which is a key factor in Scandinavian ecosystems as voles indirectly influence ups and downs in several other species populations.
In the long run, years with many voles (population peaks) are also reflected in the fox population, during the same and the following year. In general there is also a nice correlation with the dynamics of the mountain hare. When the quite easily caught voles are abundant, fox predation on other species like the capercaillie, black grouse and hares are reduced. Thus, a vole peak year favors many other small game species.
Vole photographed by Rolf Sagerstedt
Vole photographed by Rolf Sagerstedt

How is the inventory operated?

Gunnar Janson says that the survey is designed to represent the whole research area, 13000 ha. Traps (50 per plot) are placed in 20 systematically distributed plots of 1 ha each. In total, the 1000 traps are out during three days per season and are checked, and if necessary recharged, every day.

In Sweden there are several different species of small rodents. At Grimsö commonly four-five species are found and the bank vole dominates in numbers before field voles and mice species. The Vole Index, in total and for each species are presented as Catches/100 trap nights.

The national inventory of small rodents

The survey at Grimsö´s constitute along with several other locations in Sweden the sampling areas in the national environmental monitoring program of small rodents. The program is part of SLUs assignment within environmental monitoring and assessment (Foma), where Frauke Ecke at SLU in Umeå is the coordinator.

The inventory at Grimsö represents the Bergslagen region, and another location is for example Vindeln, nearby Svartberget, where the monitoring series of voles started in 1971 with 58 permanent catch plots. In addition, monitoring in the mountain region has run since 1995 in Ammarnäs with 44 catch plots and since 2001 in Vålådalen/Ljungdalen with 42 catch plots and Stora Sjöfallet with 41 catch plots.

Despite the geographical distance there are many similarities between the vole population dynamics in Grimsö and Vindeln, both regarding the cycles and the density says Frauke Ecke. Both these areas are characterized by decreasing densities primarily of field voles from 1990 until 2010, whereas the mountain areas still have large population fluctuations.

”Vole-years” occurs from time to time, what does that mean and what causes the phenomenon?

Generally we divide the population dynamic in low, in-between and peak years, so called “vole-years”, and the later ones are nowadays rare in southern and middle Sweden. However, the vole population is still cyclic in the Berslagen region but at lower densities, hence less distances between low and peak years compared to the 1970-80; ies says Frauke Ecke.

The occurrence of peak “vole-years” depends most likely on several factors that need to coincide. Overall however, it seems that winters with a lot of snow and extended snow cover provide good opportunities for voles. This might give the voles favorable conditions to hide under the snow from predators, easier access to food and they may thus reproduce almost all year around, or at least start the reproduction earlier compared to seasons with less favorable winter conditions. After a winter with a lot of snow you can expect to find more voles in the landscape.

The most recent peak years at Grimsö were 2005, 2010 and 2014, but the fluctuations show a general decrease in recent decades, says Gunnar Jansson. In the period 1988-98 (of which the first five winters can be classified as "green") Grimsö had e.g. only one medium year, otherwise very low records. The reason for why years with strong peaks have become increasingly rare in Götaland and Svealand, is generally assumed to be linked to the milder winters.

With voles comes vole fever - or?

Vole fever is acknowledged in media at times, mainly during the spring, when the garden should be cleaned, the firewood handled and so on. Vole fever belongs to the category of zoonoses, i.e. diseases carried and spread by animals to humans, a growing research topic in recent years. Both in Sweden and internationally, and an area where Frauke Ecke is active. Vole fever is caused by Puumala virus (PUUV) which has voles as its single host species. In a research project Frauke Ecke lead, voles from bio-banks caught within the national environmental monitoring in the Vindeln area was examined.
The study showed that the proportion PUUV infected animals is directly linked to the number of voles, so with more voles you have more PUUV infected animals. Moreover, it seems as a species rich small mammal fauna and presence of vole predators can counteract PUUV infection among voles. But, for still unknown reasons, the disease in humans seems to be most common in the four northernmost counties of Sweden, even though voles are common species throughout Sweden explains Frauke Ecke.

More research on voles - needs and use of data

Petter Kjellanders´ research is also linked to zoonoses and epizooties (animal diseases), the latter involves infectious diseases that may constitute a serious threat to human or animal health. From the catches made at Grimsö tissue samples of the brain, heart, lung and spleen of rodents are taken. These samples are analyzed for any tick-borne pathogens, such as Borrelia, Anaplasma and TBE-virus. Furthermore, the rodents are checked for ticks they may carry and such ticks are then analyzed for the same pathogens. Right now, the main interest is to investigate the importance of rodents for the ticks to spread Borrelia diseases. That is, is the abundance of ticks and Lyme disease prevalence in an area affected by if it is a low or peak year among rodents?

Predictions of the future population trends of voles are also important for e.g. the forestry, where especially the field vole may be a major problem in young tree plantations. These forecasts can be obtained thanks to the long-term data series collected within the national environmental monitoring.

Data from our national monitoring of small rodents have also been used internationally for various comparative studies. It has for example been shown that the prolonged decreasing of primarily Grey red-backed voles, a vole sub-species, and field voles coincides with the long-term decline in voles in other parts of Europe.

The 44th and the now approaching 45th year of the small rodent inventory

The spring 2016 showed low numbers of small rodents in Bergslagen, with a total Vole Index of  0.6 catches / 100 trap nights. In the autumn, however, it was a really good peak with 4.98 catches / 100 trap nights.

The results until the 44th season is compiled as population dynamics data freely available via Grimsö wildlife research station or SITES website. In May 2017 a new inventory round starts!
Contact:
Gunnar Jansson, Researcher and coordinator of SITES Grimsö
 
Frauke Ecke, Coordinator of the national environmental monitoring and assessment program of small rodents, located at SLU in Umeå.
 
Petter Kjellander, Professor in wildlife ecology at SLU, Grimsö Research Station.
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All SITES stations participating in SITES AquaNet meet at Erken for three days to fine tune preparations for the test experiments starting in a few weeks at each station. 

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SAFE, SITES Agroecological Field Experiment, initiated during 2016-2017, builds a unique field facility where entire agroecosystems can be studied. SAFE builds on four agroecosystems representing different cropping systems; a reference system, an organic system, a perennial system and an agroecologically intensified system. A monitoring program runs for levels and quality of yields, soil nutrient status, and soil moisture and temperature along with spectral measurements (NDVI). In this facility SITES can provide data and infrastructure for researchers to address a broad range of scientific questions and disciplines relevant for the scientific community related to ecosystem services. 
At Lönnstorp 14 ha on the most fertile agricultural land in Sweden has been divided into four blocks of cropping systems, creating the SAFE facility (Figure 1). The large area of SAFE allow large agroecosystem representation and possibilities for sub-plots with additional experiments or temporary treatments available for researchers to use in science.

Background on cropping systems and the idea of SAFE
All crops have different nutrient uptake mechanisms and different growth patterns, such as root architecture, developmental stages with different timing and different resistance for pathogens - factors that builds the foundations of cropping systems. A cropping system is defined as an ecosystem where cropping activities are done. A cropping system could be a crop rotation, where a sequence of crops grow one every year on each field or intercrops, where two or more crops in the same field at the same time are rotated to better use the soil resources and reduce success of pathogens.

Crop rotations with annual crops are common in Sweden. The related agricultural management of such systems however include practices with intensive soil disturbance which lead to loss of soil organic matter and nutrients, as well as loss of small mineral soil particles. To control pathogens outbreaks pesticides can be used too.

In the effort of developing a more sustainable agriculture SAFE was initiated as a test-base for other agricultural practices and cropping systems e.g. to include perennial plants that could protect the soils from eroding, and increase the biodiversity by creating more biologically complex systems.

Perennial crops do not need to be re-sown or tilled/ploughed every year, they also provide habitats for possibly beneficial animals, which can e.g. predate on pathogenic organisms. Perennial crops are also expected to better sequester carbon into the soil, since the roots are sustained in the system the whole year as well as year after year. The use of perennial arable crops is a highly innovative method and breeding processes are running in many parts of the world. SITES Lönnstorp cooperate with the Land Institute in Kansas, US, who is one of the leading institutions for this work. At Lönnstorp, the perennial cereal Kernza© is used as a model for perennial cereals and the agroecological implications of this type of crop are studied in the Perennial system.

Other perennials, such as fruit and nut trees, as well as different shrubs, has earlier occurred in the landscape in field borders, field islets, and close to farm buildings. In SAFE these perennials are reintroduced and incorporated in a structured way into the agricultural intensified cropping system, the Agroecologically Intensified system.

Crops host different pathogens and diversified cropping systems could lead to lower success of pathogens, that is, the host specific pathogens will suffer from not having its host in its habitat (in crop rotations) or its host is intermixed with barriers (intercropping). The population of the pathogen will not thrive, which in turn means that both the population growth of the pathogen and the damage to the host crop will be suppressed.

The management elements of rotations, intercrops and perennials are all provided and mixed in SAFE. Contemporary agroecosystems are included as well as potential cropping systems for the future, with the perennial cereal Kernza© and the structurally and functionally diverse crop rotation with shrubs and apple trees. SAFE also includes cover crops to reduce erosion and nutrient leaching as well as adding to the soil organic matter. All cropping systems and sub-plots, except one sub-plot, in the entire SAFE facility are covered every winter.
Figur 1. The SITES Agroecological Field Experiment (SAFE) with the four agroecosystems which are replicated in four blocks (A-D).
Figur 1. The SITES Agroecological Field Experiment (SAFE) with the four agroecosystems which are replicated in four blocks (A-D).
Components in SAFE
The entire SAFE consists of four cropping systems, described below and they are replicated in four blocks (Figure 1). The cropping systems run and are managed accordingly agricultural practice year around.

The Reference System (REF): corresponds to contemporary conventional crop rotation, typical for the region and includes autumn-sown oilseed rape, wheat, and sugar beet, followed by spring barley sowed with grass-legume ley which continue as a cover crop during winter after the barley has been harvested. In the reference system, all four main crops are represented every year in four sub-plots in each block. In the reference system, either the main crop is sown in the autumn or a cover crop is established, except for after sugar beet, which is harvested too late. Therefore, only one crop in the rotation is followed by bare soil during winter.
 
The Organic System (ORG): corresponds to contemporary organically certified crop rotation, typical for the region. The organic system includes two intercrops. The rotation includes spring barley-lupine intercrop; winter rye sown with grass-legume ley (functions as cover crop two winters and as main crop the summer in between; beetroot; phacelia (functions as cover crop); faba bean-spring wheat intercrop, winter oilseed rape, winter wheat in-sown with grass-legume ley (functions as cover crop two winters and as and main crop the summer in between). In the organic system, four of the main crops are represented every year in four sub-plots in each block. In the organic system, the soil is covered every winter, either by autumn sown crop or cover crop.
 
The Perennial System (PER): has perennial wheat grass Kernza© as a model for future perennial cereal crops and is grown with and without the legume Medicago sativa (lucerne). The perennial system differs from the other agroecosystems in SAFE primarily in its perennial feature and the following lower management intensity needed. This perennial system only needs soil preparation the first year of establishment, it is only cut to suppress weeds one or two times in the season, and is fertilized to lower extent (with biofertilisers) due to that roots are expected to reach nutrients to a larger depth than annual crops. No pesticides or mineral fertilisers are used in the perennial system.
 
The Agroecologically Intensified System (AI): follows the crop rotation in the organic system but with a mixture of phacelia and oil radish as cover crop after beetroot and a cultivar mix of winter wheat for increased diversity, as well as a grass-legume mixture with higher diversity than in the organic system. In the AI system, linear elements (strips) with perennial shrubs (several species as wind breaks) and trees (apple trees) add to the structural and functional diversity of the system, and are planted to fit the machine park at Lönnstorp in order to design a system that allow for rational management. In the AI system one main crop is represented, together with the perennial and structural elements, each year in each block.
Demonstration of SAFE. Photo by Hélène Hagerman
Demonstration of SAFE. Photo by Hélène Hagerman
Relevant research fields
The SAFE field facility can be used to address questions in the topics of e.g. agronomy, agroecology, economy, ecology and landscape research. The facility is important for studies of sustainability, climate change, environment, and resilience and facilitates new and existing cooperation between researchers. SAFE is also a convenient meeting place, for demonstration and education activities.
Researchers can perform studies using the plots and establish minor experiments within the experiment. It is possible to focus particular parts of the systems, analyze an entire system or use several or all of the systems for comparative studies.
 
Examples of research projects that will use SAFE:
Nutrient efficiency in different agroecosystems.
Biological control or occurrence of beneficial organisms in different agroecosystem.
Occurrence of pollinators in different agroecosystems.
Climate change manipulations in sub-plots of the facility.
Short- and long-term changes in soil quality in different agroecosystems.
Intercropping of perennial Kernza© and lucern in SAFE. Photo by Hélène Hagerman
Intercropping of perennial Kernza© and lucern in SAFE. Photo by Hélène Hagerman
SAFE monitoring program
The levels (dry weight of seeds and straw, or root and leaves for sugar beet and beetroot) and quality of yields (N and C content) are recorded annually in each sub-plot for each crop. Soil nutrient status (total soil N, P and C) are recorded at three depths (0-30, 30-60, and 60-90 cm) over the growing season every second year in each sub-plot. Soil moisture and temperature (at 3 cm depth) are recoded hourly over the growing season in each sub-plot. In block A, spectral measurements (NDVI) are done continuously over the whole year in both sub-plots of the perennial system and in the annual wheat in the reference system for SITES Spectral.

At the establishment of SAFE, soil biological, physical and chemical characterization was done. The biological characterization covered earthworms, mites, collembola and nematodes. The physical parameters covered clay, silt, sand and organic matter content (soil texture). The chemical covered soil pH, total N, P, and C; soluble P, K, Na, Ca, and Mg. For more details see the interactive map or contact any of station managers.  
Get in contact with SAFE
To access data or get information about SAFE please contact station managers Erik Steen Jensen or Linda-Maria Mårtensson. To view SAFE measurement program (parameters, types and instrumentation etc.) please survey this mapErik Rasmusson, Ryan Davidson, or William English can also assist regarding questions about SAFE.
 
How was SAFE initiated?

SAFE has been designed and developed from discussions with stakeholders, research colleagues in several disciplines, farmers, advisors and authorities. The buildup of a facility like SAFE is valuable to study and evaluate potential cropping systems for the future and the effects on the environment.  
 
Interconnections to SITES Spectral
One stationary mast with spectral sensors in the perennial system and one mobile mast follow the winter wheat in the REF system for comparison (with the perennial) are Lönnstorp part of the SITES Spectral integrating facility, two green dots in block A Figure 1. The SITES Spectral facility can be used to study water holding capacity, wind caused droughts, pathogens etc. More about SITES Spectral.

SAFE Brochure
SAFE at Lönnstorp homepage
Kernza©  in SAFE before harvest 2016. Photo by Hélène Hagerman
Kernza© in SAFE before harvest 2016. Photo by Hélène Hagerman
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During April and May 2017 are a group of students in Abisko to study arctic geoekologi. The course is given by Umeå University and tend to attract several international students.

Maria Myrstener and Gerard Rocher Ros, both of which are graduate students in the Department of Ecology and Environmental Science at Umeå University blogs about his time in Abisko and the student projects assist in.

Read more on their research blog:
Maria Myrstener – only in swedish
Gerard Rocher-Ros
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