Aquaexcel 3.0

The AQUAEXCEL 3.0 project is a new H2020 project, the successor of previous Aquaexcel projects (AQUAEXCEL from FP7 and AQUAEXCEL2020 from H2020 - https://aquaexcel2020.eu/), in which the FFPW USB is delighted to be a partner.

The AQUAEXCEL 3.0 project was launched on 1st November 2020 and will continue until October 2025. This H2020 project is funded by the European Commission and coordinated by Dr. Marc Vandeputte from INRAE France.

The AQUAEXCEL 3.0 project integrates 40 top-class European aquaculture research facilities that will provide a world-class platform for aquaculture research, from biology to technology, in all types of rearing systems, covering all major EU farmed fish species as well as the most promising new species, i.e. shellfish, macroalgae, and recyclers.
For more information on the project, please see www.aquaexcel.eu.

The project has two main parts. The major one is Transnational Access (TNA) which enables to use the infrastructure of the project partners through small research projects. The second part is the collaborative research focused on the improvement of infrastructure practices and services.

22 TNA projects with 100 weeks of access shall be implemented within the FFPW USB´s installations during the project´s duration.

Operating institution: University of South Bohemia in České Budejovice, Faculty of Fisheries and Protection of Waters (JU)
Type of Operating institution: University

Research infrastructure JU has 4 installations:
1. Institute of Complex Systems (ICS)
2. Institute of Aquaculture and Protection of Waters (IAPW)
3. Intensive Freshwater Aquaculture Units (IFA)
4. Laboratory of Fish Genetics and Reproduction and Hatchery (GRC)

Location:
GRC and IFA – Vodňany, ICS – Nové Hrady, IAPW – České Budějovice, Czech Republic

Contacts:
Scientific contact: Petr Císař, Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.
Administrative contact: Monika Malkusová, Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.

Installation managers:
ICS - Petr Císař, Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.
IAPW – Jan Mráz, Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.
IFA – Oleksandr Malinovskyi, Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.
GRC – Vojtěch Kašpar, Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.

Researchers from any EU or Associated country can apply for access to any of the AQUAEXCEL3.0 Research Infrastructures. Applications must be made to use a Research Infrastructure in a different country than that of the lead researcher. Details of the other Research Infrastructures available within AQUAEXCEL3.0 can be found on www.aquaexcel.eu and on each institution's website.

Access to the facilities is provided free of charge to users and travel and subsistence expenses are also paid. In general, it is anticipated that access will be in the form of one or in some cases two scientists travelling to work at one or more installations within the Research Infrastructure for a maximum period of 90 days (more information in Modality of Access).

Applications for Transnational Access may be made by any organisation (including commercial companies), but the conditions of access require the results of the work to be published and made available to the scientific community via standard channels. If the FFPW USB is in the author´s team, then open access to publications as well as research data must be enabled.

Applications for Transnational Access shall be made in accordance with the guidance published in the “Call for Proposals” that is made available on the project website www.aquaexcel.eu. Applicants are also encouraged to directly contact individual facilities to discuss their research plans in advance of submitting an application.
Applications for Transnational Access will be reviewed by an expert selection panel and an independent ethics adviser. Projects selected for Transnational Access will be expected to demonstrate high scientific quality, make efficient use of resources, and effectively address issues important for the development of European aquaculture – e.g. as expressed through the Strategic Research Agendas of the European Aquaculture Technology and Innovation Platform (www.eatip.eu).

All Transnational Access projects must be carried out between 2021 and October 2025. The call for access will be permanent during the project´s duration with specific cut-off dates for the selection.

ICS: A variety of automated monitoring systems are offered to perform ethological experiments or experiments focused on the fish welfare of fish appearance monitoring. The RAS system and several aquarium systems are available for the experiments. A camera-based fish monitoring system enables us to get information about fish behaviour automatically. Hyperspectral imagery can be used to analyse fish mean (consistency and structure). Fish colour analysis serves to measure the differences between diverse diets used for fish breeding. The user is the researcher who needs to perform fish experiments with automatic behavioural or appearance data collection, processing, and analysis.

IAPW: It offers a wide range of analytical services related to fish and feed quality, fish nutrition and early ontogenesis of fish as well as feeding trials, culture of new fish species etc. The innovation of fish products recipes, marketing research, storage conditions, meat yield of specific species and so on are provided. The laboratory developed a patented technology to produce carp with increased content of omega 3 fatty acids. Another key area is the technology of intensive aquaculture and the early ontogeny of economically important or protected species and species of interest to sport fishing.

IFA: This installation offers fish culture under RAS and pond conditions related to larval, juvenile, ongrowing, grow-out and broodstock stages, technical support and routine biological examinations for exact and precise experiments related to environmental stimulation of gametogenesis and final reproduction in broodstock, fish nutrition and feeding, optimization of fish husbandry, optimization of cultured conditions during all phases. Laboratories are enabled to assess the effects of xenobiotic on biochemical, chemical, haematological indices and histopathology in fish and crustaceans. Service/support of this installation will observe changes in the tissues of fish and crayfish exposed to tested substances on the level of gene expression and thus help us assess possible negative effects of these substances on the exposed organisms with high sensitivity.

GRC: This installation is focused on reproduction-related experiments - broodstock management and the preparation for semi-artificial or induced reproduction, work with fish gametes, the study of fish sperm motility, cryoconservation of fish gametes, flow-cytometry, light or fluorescence microscopy, image analysis, micromanipulations, genetic analyses (sequencing, fragment analysis, semiconductor sequencing).

ICS – Access consists of the analysis of the research problem or dataset followed by the proposal of the best solution supported with the testing of different methods for data query, processing, and analysis.

IAPW – The unit of access consists of the preparatory work, experimental and instrumental facilities, and analytical services related to fish and feed quality, fish nutrition, processing, and product development, intensive fish culture, and early ontogenesis, aquaponics.

GRC – The unit of access consists of the preparatory work, reproduction of fish, incubation of fertilized fish eggs or work with fertilized gametes (analyses or micromanipulations), cryoconservation of fish sperm, juvenile breeding of hatched embryos, or analyses of obtained samples in genetic labs.

IFA - Specific training courses and performance of experiments related to fish handling and nutrition, biometric of fish, stripping of gametes, evaluation of sperm or egg quality, preparation of experimental food, assessment of larval and juvenile quality, optimization of culture in larvae, juveniles and other stages, evaluation of the physiological status of fish, behaviour observation, determination of survival and deformities etc.

JU will provide suitable supervision and guidance for potential inexperienced users to properly carry out the work. The technical and management staff will be helpful with the overall project´s implementation.

Director of ICS and Installation manager within AE3.0 project:
Dipl.-Ing. Petr Císař, Ph.D.
Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.
+420 38 777 3802
+420 724 219 003

Address: Zámek 136, 373 33 Nové Hrady
Website of the ICS: https://www.frov.jcu.cz/en/faculty/faculty-parts/institute-of-complex-systems

General description:
The Institute of Complex Systems was established as one of the three institutes of the Faculty in 2012. The main aim of the Institute is research in the field of complex systems and the creation of a full circle starting from experimental design, moving over to experimental realization, data processing and analysis, and finally the management of data. This vision is very broad and therefore all the laboratories are involved in mutual cooperation. We can find complex systems all around us. An example of a complex system is an anthill, human management, social structures, climate, nervous systems, cells and living creatures as well as energy and telecommunication infrastructure. The modern trend is the exploration of complex systems.
To be able to identify these systems, it is necessary to combine the methods from different scientific fields. It is necessary to measure the system (in the form of a controlled experiment), gather the knowledge through data processing of experimental data, determine the description of system behaviour, draw conclusions, and evaluate them using a reproduction of the experiment. This is the way how to identify complex systems, how we can predict their behaviour and control them. The Institute is directly connected with the Faculty through the joint research projects focused on the analysis of the behaviour of aquatic organisms and management of experimental data.

Technical description:
The Institute of Complex Systems is active in the applied research in aquaculture monitoring systems. The Institute builds on the mathematical, physical, chemical, and cybernetic background and applies the knowledge in biology. Several state-of-the-art devices (hyperspectral imagery, atomic force microscopy) and developed devices (3D camera-based fish behaviour monitoring, fish appearance analysis) are available for the experiments from aquarium scale to fish tank scale. The new experimental tank equipped with video cameras and a monitoring system is also available to get new information about fish and fish school behaviour. These methods of image and signal processing and multidimensional data analysis can be accomplished for challenging research.

Remote monitoring & control:
This is designed to perform remote monitoring of fish behaviour and appearance. Water quality parameters, pH, temperature, and dissolved oxygen content (DOC) in water can be automatically registered. Different camera systems (standard camera, infra-red camera, hyperspectral camera, UV camera) are used to monitor the fish. These values are monitored and stored for possible future computer processing.

Water and environmental conditions:
Tap water is used for RAS and aquarium systems. All cultivation conditions are controlled. The experiments are operated as laboratory experiments on a small scale.

Flowrate:
The maximum flow rate through the rearing station is calculated at 10.5 l.s-1

Temperature:
The heating of water in the recirculation system is currently implemented by using the space heating temperature control air conditioning.

Salinity:
It is a freshwater system.

Oxygen:
Dissolved oxygen content is automatically registered.

pH:
The pH is automatically registered.

Light intensity and wavelength:
Light intensity and wavelength are not manipulated or automatically registered.

Photoperiod:
The photoperiod is not manipulated or automatically registered.

Fish measurements:
Size, weight, tagging (classical or P.I.T.) can be recorded, behaviour and fish appearance can be monitored in special systems.

Director of IAPW:
Dipl.-Ing. Jan Kašpar
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+420 38 777 4678
+420 734 269 085

Installation manager within the Aquaexcel3.0 project:
Assoc.-Prof. Dipl.-Ing. Jan Mráz, Ph.D.
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+420 38 777 4643
+420 737 221 913

Address: Na Sádkách 1780, 370 05 České Budějovice
Website of IAPW: https://www.frov.jcu.cz/en/faculty/faculty-parts/institute-of-aquaculture-and-protection-of-waters

General description:
The Institute of Aquaculture and Protection of Waters (IAPW) in Ceske Budejovice is an application-oriented institution that offers students and researchers specialization in the fields of fish farming, fishery, fish quality, hydrobiology, and water protection. The IAPW consists of 2 laboratories (The Laboratory of Controlled Fish Reproduction and Intensive Fish Culture and The Laboratory of Nutrition), a fish processing plant, and a fish shop. Laboratories deal with a wide range of research and consulting activities in the areas of pond and intensive aquaculture, processing, and fish quality, fishery in open waters, hydrobiology, and water protection.

Technical description:
The IAPW comprises an aquaponic hall, two analytical labs, four aquarium rooms, and a processing plant. The analytical part consists of two fully equipped laboratories with instruments for proximate and amino acid analyses, sensory analyses, lipid, volatiles and oxidation analyses, vitamin and protein analyses, elemental analyses, and microscopy analyses. The aquaponic hall consists of 6 independent RAS and 200 m2 of greenhouse.

See more details on individual parts of the IAPW:

• Aquarium rooms with RAS systems
• Fish processing plant
• Aquaponic hall

Installation manager within the Aquaexcel3.0 project:
MSc. Oleksandr Malinovskyi, Ph.D.
E-mail: Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.
tel: +420 389 034 770

Mailing address: Zátiší 728/II, 389 25 Vodňany
Contact address: Rechle 1336, 389 01 Vodňany

Websites of laboratories /workplaces associated within the IFA installation:
> Laboratory of Intensive Aquaculture - https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/laboratory-of-intensive-aquaculture
> Laboratory of Aquatic Toxicology and Ichtyopathology - https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/laboratory-of-aquatic-toxicology-and-ichtyopathology
> Experimental Fish Culture and Facility - https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/experimental-fish-culture-and-facility

General description:

The Intensive Freshwater Aquaculture Units (IFA) includes:
1) Two experimental rooms for controlled larval and juvenile culture can be used for different experiments with optimization of nutrition, environment conditions (temperature, light, oxygen, pH), fish density, polyculture stock, frequency of feed application, and the daily feeding rate using an automatic self-feeder from the Imetronic company, etc. to study the effect of the mentioned parameters/conditions on the efficiency of larval and juvenile culture in different high-valuable fish species such as pikeperch, perch, largemouth bass, grayling, Danube salmon, African catfish, etc. Each system is equipped with modern experimental RAS including all technical components with a total water volume of 6 m3 and 9 experimental tanks (each with 350 litres).
2) One fish culture chamber for controlled environmental stimulation (temperature, light regime, and feeding regime) of out-of-season or normal season reproduction in different fish species broodstock is equipped with modern RAS including experimental tanks (4 and 6 tanks with each volume 1.2 m3 and 350 litres, respectively), mechanical and biological filtration, degassing, oxygen saturation and ozone water treatment saturation.
3) Large scale RAS hall for intensive aquaculture of ongrowing or grow-out stock of different species includes two separated RAS, each system with a total water volume of 30 m3 and controlled temperature, light, pH and oxygen conditions and the possibility to use ozone treatment for water sterilization. Each RAS system has 10 experimental tanks with an average volume of 1.2 m3 and can be used for different large-scale experiments related to the optimization of intensive aquaculture (for example: nutrition, environmental conditions, water quality, fish density, stock etc.) in ongrowing or grow-out stock of different species (for example: pikeperch, perch, largemouth bass, grayling, Danube salmon, African catfish etc. ).
4) Laboratory of mass rotifer production can be used for controlled mass production of freshwater (Brachionus calyciflorus) or marine rotifers (Brachionus plicatilis). This laboratory is equipped with a batch or a continuous RAS production system from the Pentair company and an experimental aquarium system where different nutrition aspects of the first exogenous feeding can be tested in a larval culture of different fish species such as pikeperch, burbot, tench or some ornamental or marine fish species.
5) Haematological and biochemical laboratory is equipped with complete facilities for the analytical analyses of chemical, biochemical, haematological parameters (ultracentrifuge, double-beam spectrophotometer SPECORD 210, plate-reader with fluorescent and luminescent module Infinite M200PRO (TECAN), VETTEST 8008 analyser, analyser of blood gases Radiometer ABL90 Flex, real-time PCR, PCR thermocycler, NanoDrop). This installation can be used for different biochemical and hematological analyses from different aquaculture, physiological and toxicological studies.
6) Histological laboratory is equipped with the tissue processor Histomaster 2052/1.5, modular tissue embedding center - Leica EG1150, semi-automatic rotary Microtome, automatic slide staining system - TISSUE-TEK® DRS™ 2000, SEKURA, contrast and fluorescence microscopy. Also, this installation can be used for different tissue analyses from different aquaculture, physiological and toxicological studies.
7) Hatchery for broodstock management, egg incubation, and hatching of larvae is equipped with tanks and other facilities which can be used for broodstock management and reproduction. Also, this hatchery can be used for egg incubation and larval hatching in different types of jars or incubators. The hatchery can use the water supply from the flow-through or recirculating system. In this way, the water temperature during egg incubation can be easily controlled.
8) Pond culture system includes a maximum of 9 experimental ponds with a total area of 0.16 or 0.08 ha, which is supported by water from the river Blanice, that can be used for the optimization of larval, juvenile, or marketable mono- or poly- culture of different fish species.

Technical description:

Remote monitoring & control:
All RAS systems are continuously controlled by different sensors (water level, oxygen saturation, pH, and temperature). All values are stored for possible future computer processing.
Pond culture has the character of the outside and an uncontrolled aquaculture system with natural fluctuating parameters.

Water and environmental conditions:
Only springs, drinking, and underground water supply are used for daily water exchange with a maximum 5-10% rate. Different water flow rates with different oxygen saturation, pH, temperature can be used during using of these systems.

Salinity:
Freshwater is mainly used with the possibility to increase salinity up to 2-5 ppt in RAS facilities.

Oxygen:
Normally 100% oxygen saturation is used with the possibility of decreasing or increasing of this level. Oxygen saturation is measured and controlled twice per day.

pH:
Normally a pH between 6.8-7.2 is kept with the possibility of decreasing or increasing of this level. The pH is measured and controlled twice daily.

Light intensity and wavelength:
Between 80 – 400 lux of light intensity is kept with a different light regime.

Photoperiod:
The light regime is possible to be controlled with a minimal interval of 15 minutes of light or dark.

Fish measurements:
Fish size and weight will be recorded. Also, fish tagging is possible to organize by classical – fin cutting or PIT tags.

Installation manager (GRC) within the Aquaexcel3.0 project:
Dipl.-Ing. Vojtěch Kašpar, Ph.D.
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+420 387 774 609

Address: Zátiší 728/II, 389 25 Vodňany
Websites of laboratories /workplaces associated within the GRC installation:
> Laboratory of Germ Cells: https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/laboratory-of-germ-cells
> Laboratory of Molecular, Cellular and Quantitative Genetics: https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/laboratory-of-molecular-cellular-and-quantitative-genetics
> Laboratory of Reproductive Physiology: https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/laboratory-of-reproductive-physiology
> Genetic Fisheries Center: https://www.frov.jcu.cz/en/faculty/faculty-parts/research-institute-of-fish-culture-and-hydrobiology/genetic-fisheries-center

General description:
The Laboratory of Fish Genetics and Reproduction and Hatchery (GRC) is a modern and multipurpose fish hatchery (with the possibility of farming early fish stages, indoor tanks for preparation of broodstock for controlled reproduction, experimental fish rearing in special troughs, and for work with young brood fish) with a total area of 220 m2. Tap water is used for egg incubation and fry nursing, two recirculation systems are cleaned through biofilters and sterilized by ozonisers and UV radiation. Water levels, water temperatures, and oxygen saturation with control of preparation of technological flowing through or recirculated water are monitored in the entire system with the use of technological reporting using GSM technology. Twelve circular tanks (6m3 in total) and four rectangular basins (12m3 in total) operated by two separated recirculation aquaculture systems (RAS) are used for rearing the yearlings. Two RAS (2 x 8m3) are ready for experimental preparation of broodstock for controlled reproduction. The Laboratory of Reproductive Physiology is well equipped with microscopy and equipment for analysis of fish spermatozoa motility, cryopreservation experiments, and semen analysis. The Laboratory of Germ Cells is equipped with instrumentation for germ cell and blastomere cryopreservation and micromanipulation and the Laboratory of Molecular, Cellular and Quantitative Genetics is well equipped with aquaria rooms, microscopic and imaging systems, fluorescence microscopy, and LSM Fluoview confocal microscopy, Partec flow cytometry, multichannel flow cytometry, DNA laboratory (e.g., PCR, gel electrophoresis and DNA sequencers - automated sequencing, semiconductor sequencing).

Technical description:
The hatchery is modern and multi-purpose – it consists of a room with several tanks for storage or preparation of spawners for artificial reproduction, a room for incubation of eggs and keeping fingerlings, specific experimental incubators for experimental work based on fertilization experiments. The installation is closely connected with laboratories for experiment set-up, control, or evaluation.

Remote monitoring & control:
Water levels, water temperatures, and oxygen saturation with control of the preparation of technological flow or recirculation water is controlled and the status is reported using GSM technologies if needed.

Water and environmental conditions:
River water necessary for roe incubation and farming of fingerlings is cleaned through a micro-screen filter, an ozonizer, and is sterilized by UV radiation. The hatchery system is supplied with water from a water pipeline system with recirculation through biofilters. Water for spawners, egg incubation, or fingerlings is heated to the required temperature in three mutually independent reservoirs.

Temperature:
Water for spawners, egg incubation, and fingerlings is heated to the required temperature in three mutually independent reservoirs. The water temperature in the system is dependent on the outside temperature but can be slightly warmed or cooled (on a small scale) according to the actual needs. Temperature manipulations can be implemented in small recirculation systems according to the needs of the experiment.

Salinity:
It is a freshwater system.

Oxygen:
Dissolved oxygen content is automatically registered.

pH:
pH is not registered automatically.

Light intensity and wavelength:
Light intensity and wavelength are not manipulated or automatically registered.

Photoperiod:
Photoperiod is not manipulated or automatically registered.

Fish measurements:
Size, weight, tagging (classical or P.I.T.) can be recorded, the behaviour can be monitored in special systems

Duration of work: Each user or user group is expected to stay on average:

>14 days at the IAPW - feeding trials, analyses of feed and fish quality, fish processing, optimization of fish intensive culture, aquaponics
>14 days at the ICS - typical access starts with the analysis of the research problem/data, continues with the proposal of the solution and development of the solution of particular data
>14 days at the GRC - preparation of broodstock, the realization of experiments related to reproduction, physiology of reproduction, genetics, incubation of fertilized eggs and juvenile breeding, preparatory work in the laboratory – preparation of samples, equipment set-up, calibration or operation, laboratory experiments or analyses, cryoconservation of gametes, etc.)
>14 days at the IFA - specific training and performance of experiments related to fish handling and nutrition in intensive farming of high-value fish, their reproduction including stripping of gametes, evaluation of sperm or egg quality, preparation of experimental food, assessment of larval and juvenile quality, optimization of culture in larvae, juveniles and other stages, evaluation of the physiological status of fish, behaviour observation, determination of survival and deformities, biometric of fish etc.; preparatory work-related experiment and set-up of experimental design, preparatory work in the laboratory – treatment of samples, equipment calibration and measurement on the analytic instrument.

Unit of access: one week (for all 4 installations)

One typical access consists of:

>2 units of access for GRC and ICS
>4 to 20 units of access for IFA
>2 to 12 units for IAPW.

The difference in the number of units is influenced by the type of experiment and used facility, i.e. generally in ponds and tanks the project will last 8-20 weeks whereas the length of a lab experiment is just 2 weeks.

Location of work: Vodnany (GRC and IFA), Ceske Budejovice (IAPW) or Nove Hrady (ICS)