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LIST OF THE DISSERTATION TOPICS AND POSSIBLE SUPERVISORS

Proposed dissertation themes for the Doctoral degree Studies in
Ecology and Environmental Science at Klaipėda University

Study period: 2017-2021.

The doctorate study program in Ecology and Environmental science aims at development of marine natural sciences. Investigations are focused on interaction of natural and anthropogenic processes in the marine and coastal environments. The complexity of the research objects determines wide variety of scientific problems to explore; it requires consolidation of the interdisciplinary research potential. The doctorate study program provides excellent research opportunities for geographers and geologists, physicists and chemists, mathematicians and computer scientists, environmental engineers, and, of course, biologists and ecologists. The strategic research areas are following:

  • Natural marine and coastal resources and ecosystem services under to global change conditions.
  • Integrated coastal zone management and marine spatial planning for sustainable development of coastal and maritime economic development.
  • Development of innovative monitoring, data management and modeling methods and their application for forecasting and management of marine and coastal processes.

The proposed dissertation themes are defined in a framework of the above strategic research areas.

Brief description of the topic Marine litter is a growing problem in the marine environment. To improve the present situation, the EU Marine Strategy Framework Directive (MSFD) demands, that ‘Properties and quantities of marine litter do not cause harm to the coastal and marine environment’. ‘Therefore, it is necessary to develop monitoring methods for the identification and trends in the amount of litter washed ashore and/or deposited on coastlines, including analysis of its composition, spatial distribution and where possible source’ (MSFD 2008/56/EC). The research shall support the implementation of the MSFD in Lithuania and the Baltic region and shall focus on the meso- (5-25 mm) and large micro- (1-5 mm) plastic fraction. Objectives are:

a) to test and further-development cost-effective monitoring methods and strategies,

b) the development of meso- and microplastic indicators and thresholds for a good status of the marine environment,

c) the exemplary assessment of meso- and microplastic avoidance measures.

Requirements for a candidate The candidate should have a good knowledge of aquatic ecology or related fields and the capability to work in an inter-disciplinary research environment as well as very good English language skills.
Existing research experience The supervisor, G. Schernewski, is author of 100+ publications on coastal and marine issues, including several international publications on marine litter. He is coordinator of the BONUS-project BaltCoast and had coordination tasks in international projects like CHARM, OURCOAST, SPICOSA, AMBER, SUSTAIN or GENESIS. He is involved in several projects on marine litter namely UBA-Marine Litter, Mikromik, Micropoll and MicroCatch. Further, he serves as international expert for e.g. EU, EEA, UNEP, UNESCO and HELCOM and is member of the national expert group on marine litter. His working groups in Lithuania and Germany are dealing with the topic already for several years.
Existing research infrastructure The research is cooperation between Klaipėda University and the Leibniz-Institute for Baltic Sea Research, Germany. The research infrastructure, laboratory and field equipment as well as methodological approaches are available (e.g. infrared microPHAZIR, Separator). The research will be carried out within the BONUS project MicroPoll and the BMBF project MicroCatch. The projects ensure complementary funding and an international research environment.
Potential supervisor Prof. dr. habil. Gerald Schernewski, gerald.schernewski@io-warnemuende.de

www.io-warnemuende.de/bio-ag-coastal-marine-management.html

Brief description of the topic Coastal waters of the Baltic Sea are suffering from the high nutrient loads from the catchments resulting in eutrophication and intense cyanobacteria blooms. Cyanobacteria are known to produce diverse secondary metabolites and other compounds, which could be toxic not only for the water organisms, but also for humans. This project is aimed to delineate the spatial and temporal trends of cyanobacterial blooms (including diversity of whole phytoplankton species composition) in the Lithuanian coastal waters, to assess both the potential harm and value of secondary metabolites and other compounds produced by cyanobacteria in biotechnology applications, as well as to evaluate toxicity of dominating cyanobacteria species according the specific genes.
Requirements for a candidate Educational background in the water ecology, phytoplankton ecology and systematics, toxicology and already existing experience in laboratory work are required. English proficiency would be a good asset too.
Existing research experience The candidate will join research team working in this field. The topic is well related to the ongoing EU COST project EUAlgae (European Network for Algal-Bioproducts, 2015-2109).
Existing research infrastructure This work will be supported by the research projects of KU and Institute of Oceanography, Gdansk University (GU, Poland). There is possibility to use KU laboratory facilities, as well as there are possibilities to do traineeship and use facilities for the identification of cyanobacteria secondary metabolites at the Marine Biotechnology department of Institute of Oceanography (GU). The submitted national research project (The consequences and use of cyanobacterial blooms in the changing coastal environment) is closely related with the proposed topic.
Potential supervisor Dr. Renata Pilkaitytė (renata.pilkaityte@apc.ku.lt; 846-398814)
Potential scientific advisor Prof. Hanna Mazur-Marzec (University of Gdansk) (biohm@ug.edu.pl)
Brief description of the topic The project is aimed at studies of diversity-ecosystem functioning (D-Ef) and diversity-stability (D-S) in estuarine environment. The work will be largely based on laboratory experiments in which microcosms mimicking shallow estuarine ecosystems will be realized, based on three main hypotheses:

1) oversimplified experimental and statistical approaches do not allow to analyze complex communities establishing complex network of processes;

2) functional more than species diversity of macroinvertebrates promotes efficient coupling between microbially-mediated N-processes and primary producers activity;

3) microbial, macroinvertebrate and primary producers diversity buffer environmental perturbations as cultural eutrophication and climate-change related altered hydrology, nutrient delivery and temperature.

An increasing number of “benthic actors”, resulting in the co-occurrence of different macroinvertebrates functional groups and primary producers growth forms, will be added to microcosms containing different sediments, along organic gradients. This project is is based on field work, microcosm experimentation and modeling, and combines microbiological and biogeochemical tools.

Requirements for a candidate The candidate should have good knowledge in benthic ecology and biogeochemistry, laboratory experience, experience in data analysis using statistical tools, good knowledge of English language and capacity to work in research groups.
Existing research experience The topic is tightly related with two other PhD proposals, targeting macrofauna and primary producer communities and their experimental manipulation under controlled conditions, and with ongoing research activities of the benthic biogeochemistry team in the Marine Science and Technology Center (Klaipeda University).
Existing research infrastructure The work will be supported by scientist, facilities and laboratories of Klaipeda and Parma Universities, in the frame of ongoing collaborations between the two units. Analogous experiment can be performed along a latitudinal gradient on a shallow eutrophic (and much warmer) Italian Estuary (Sacca di Goro Lagoon).
Potential supervisor Dr. Marco Bartoli and dr. Mindaugas Žilius
Brief description of the topic Seabed images are increasingly being used to assess the sediment type, to identify and estimate quantitative distribution of marine species and benthic habitats. Modern underwater survey equipment produces vast amounts of video material. It is difficult to review and analyse this material by non-automated methods. That in turn obscures it use for routine environmental monitoring. Therefore, the automated decision-making methods, which help to process large amounts of visual information in an objective and accurate way, are needed for registration of quantitative and qualitative changes in the seabed. The aim of the study is to develop methods for automatic object detection and classification in seabed video images. Main tasks of the study:

·         creation of feature extraction methods capable to exploit information on colour, texture, shape, and geometry of image segments;

·         methods for automated detection, analysis and classification of seabed objects;

·         methods for automated analysis and classification based on committees of models;

·         techniques for information fusion, interpretation of analysis results, decision visualization, and assessing the certainty of decisions.

Requirements for a candidate Especially good knowledge of statistical methods and their applications; skills in working with MATLAB and other mathematical packages, a common understanding of the multidimensional scale, support vector machines, artificial neural networks, fuzzy logic, and random forest methods.
Existing research experience The work could take place under a tripartite agreement between KU, Kaunas University of Technology (KTU), and the doctoral student. Studies could be coordinated with the ongoing KTU programs in the Informatics Engineering area.
Existing research infrastructure Members of the KTU Computational intelligence research group have long experience of research in such fields as machine learning, pattern recognition, decision making, classification, fuzzy logics, support vector machines, random forests, and image and signal analysis. KU specialists have been involved in underwater biological research since 1993 and have good knowledge on sea bed landscape features which may be used for automated image recognition.
Potential supervisor Prof. habil. dr. Sergej Olenin, sergej.olenin@jmtc.ku.lt

prof. dr. Adas Gelžinis, adas.gelzinis@ktu.lt

Brief description of the topic Coastal food webs are currently impacted by altering climate and anthropogenic pressures, such as the introduction of non-indigenous species (NIS). Colonization by novel organisms can affect the diversity and trophic dynamics of local communities, with consequences to the health of the ecosystem. The early stages of colonization might be undetected by the current Baltic monitoring programs due to the temporal and spatial variability of the invasion process and to low abundances of the new species. For the development of an alternate monitoring tool, the PhD student will examine and test the potential of PCR-based detection of NIS via environmental DNA (eDNA) exemplified for non-indigenous species recently invaded the Baltic Sea. Their specific eDNA detection and quantification will be evaluated in laboratory incubation experiments. Optimized PCR and quantitative PCR (qPCR) protocols will be applied to known density gradients of these species along the Baltic coastline, and specific eDNA abundances compared to traditional, morphologically-based, quantifications. The outcome of this PhD thesis will be a validated workflow describing a fast, reliable and cost-effective eDNA approach to detect and identify NIS. This workflow has the potential to improve early detection and rapid response systems of existing MSFD and HELCOM monitoring strategies for the Baltic Sea.
Requirements for a candidate The candidate should have good knowledge in molecular biology; good understanding of aquatic ecology is of advantage. The candidate needs the capability to work in an inter-disciplinary research environment and very good English (or German) language skills.
Existing research experience The supervisor, M. Labrenz, is author of 60+ international publications on marine/environmental microbiology and molecular biology. The last 5 five years he was/is PI or Co-PI of 10+ national and international projects as BONUS AFISmon, BONUS BLUEPRINT, INA (development of new molecular tools in collaboration with Baltic Sea or Chinese scientists), MikrOMIK, BONUS MICROPOLL (role of microbial biofilms on microplastics), or ECOLOC, VibrioMV (relevance of Vibrios in anthropogenic influenced systems).
Existing research infrastructure The research is a co-operation between Klaipėda University, Thünen Institute of Baltic Sea Fisheries, Germany (contact person: D. Oesterwind), and the Leibniz-Institute for Baltic Sea Research, Rostock Germany. The research infrastructure, laboratory and field equipment as well as methodological approaches are available (e.g. S1, S2 laboratories, Baltic Sea cruises and traditional monitoring). The Environmental Microbiology group of ML ensures complementary funding and an international research environment.
Potential supervisor PD. Dr. habil. Matthias Labrenz, matthias.labrenz@io-warnemuende.de

http://www.io-warnemuende.de/environmental-microbiology.html

Brief description of the topic Macrophytobenthos species are generally considered good bioindicators of coastal ecosystems since vegetation is constantly impacted by water hydro-chemical, hydro-physical conditions and trophic level. Most of macrophytobenthos species together with other benthic organisms form habitats of European importance, spawning and nursery grounds for commercial important fishes.

In respect of European Directives, the development and testing of indicators based on macrophytobenthos is highly needed due to these issues:

– parameters of many indicators do not include metric of species diversity;

– there are number of proposed indicators (e.g. MARMONI project) that need testing;

– limited attempts to test universality of indicators;

– the parameters and thresholds of existing indicators greatly vary among countries;

– a lack of experimental testing of revealed empirical relationships between indicators and human induced pressures.

Hence, this study is aimed at developing or adopting robust benthic quality multivariate indices based on macrophytobenthos to reflect ecosystem changes.

Requirements for a candidate Required basic knowledge of fundamental hydro-physical, hydro-chemical and biological processes in the coastal and estuarine waters, which influence benthic vegetation. Desirable good knowledge of statistical methods and their applications, especially for statistical modelling of species distribution; experience in performance of experiments; skills with GIS methods.
Existing research experience The assessment of the red alga (Furcellaria lumbricalis) distribution patterns and its ecological role (Bučas et al., 2007; 2009; 2013) was already implemented by 3 international projects: EU FP6 project MARBEF (GOCE-CT-2003-505446), Life Nature BALTIC MPA’s (LIFE 05 NAT/LV/000100) and BONUS + PREHAB (BONUS-163). The development of indicator based on macrophytobenthos and its intercalibration was performed within EU WFD  geographical intercalibration (Baltic GIG) project. Recently, the diversity and distribution of submerged vegetation in the Curonian Lagoon were assessed applying acoustic methods (Bučas et al., 2016) within the national project – MAURAKUMA (MIP-14210). The suggested topic is related to the activities of EOMORES project (Horizon 2020, 687412), where water quality indicators are being developed using Earth Observation-based data for operational inland and coastal ecological water quality monitoring.

This PhD topic will be connected with the PhD themes on “Indicatory value of estuarine littoral benthic macrofauna… ” (proposed by D. Daunys) and “Interactions and novel approaches to disentangle benthic nutrient cycling…” (proposed by M. Bartoli, M. Zilius).

Existing research infrastructure At the Klaipėda University there are available existing material of underwater video and SCUBA divers’ descriptions; laboratories with infrastructure (e.g. microscopes, oven and scales); unmanned aerial vehicles; underwater video systems and SCUBA equipment; computer classes with softwares of GIS and statistics.
Potential supervisor dr. Martynas Bučas martynas.bucas@jmtc.ku.lt; +370 46 398878
Brief description of the topic Estuaries and lagoons are known as very dynamic ecosystems where freshwater, brackish and marine organisms of a different tolerance to eutrophication are colonizing benthic communities. Due to prevalence of highly tolerant species and extremely low diversity of macrofauna communities sampled by means of traditional monitoring, most of the studies in oligohaline lagoons failed to develop robust and reliable benthic quality indices. On the other hand, vast and heterogeneous littoral areas of these ecosystems support highly diverse benthic communities, which typically remain unsampled during traditional monitoring surveys but potentially provide higher diversity of disturbance signals compared to those in the open and deeper waters. Hence, this study is aimed at developing or adopting robust benthic quality multivariate indices to reflect ecosystem changes exploring littoral macrofauna. At the same time, higher taxonomic diversity of littoral communities insists greater functional contribution to the ecosystem processes (e.g. nutrient cycling), therefore these communities are particularly suitable for testing links between biodiversity (complexity) level and functional role. This may provide useful extension for a status assessment indices if their values are calibrated with extent of changes in important functional processes (e.g. denitrification rates, phosphate release from sediment etc.). So far, benthic ecology is restricted to the traditional validation of numerous benthic indices with static ecosystem attributes (e.g. water column Chl a or total nitrogen), while relationships between multivariate benthic quality indexes and functional characteristics are extremely rare.

This work will be primarily focused on the Curonian lagoon, but may have a clear comparative aspect with selected Mediterranean and/or Black Sea water bodies. Tasks are to a) develop and validate multivariate benthic quality assessment tool based on structural characteristics of estuarine littoral macrofauna communities; b) test multivariate benthic quality assessment tool against selected functional characteristics; c) investigate validity of relationship between multivariate benthic quality assessment tool and selected functional characteristics in different enclosed water bodies.

Requirements for a candidate The candidate should have good knowledge in benthic ecology, laboratory experience in taxonomic analysis of bottom macrofauna, experience in data analysis using multivariate statistics and good knowledge of English language.
Existing research experience The topic is tightly related to ongoing research activities of the benthic group in the Marine Science and Technology Center (Klaipeda University). Existing research experience relies on the long-term studies of the Curonian lagoon, development of benthic quality assessment tools during earlier phases of WFD and MSFD implementation and tight co-operation with leading benthic research groups in the Baltic region (Leibnitz Baltic Sea Research Institute, System Ecology Department in Stockholm University, Finnish Environmental Institute, Estonian Marine Institute etc.). This PhD topic will be connected with the PhD themes on “Development and testing of macrophytobenthos indicators… ” (proposed by M. Bučas) and “Interactions and novel approaches to disentangle benthic nutrient cycling…” (proposed by M. Bartoli, M. Zilius)
Existing research infrastructure The work will be supported by scientist, facilities and laboratories of Klaipeda, Parma and Ferrara Universities, in the frame of ongoing collaborations between the units. The thesis is planned to contribute to the implementation of WDF and MSFD in Lithuania.
Potential supervisor Prof. Dr. Darius Daunys, E. A. Fanno
Brief description of the topic The increasing human population, industrialization, intensive a land use and climate change enhanced pressure on water ecosystem functioning and therefore requires a sustainable water management. Knowledge about the state of inland and coastal water bodies are therefore of great interest and it is being monitored. A number of European legislations aiming to protect and/or to improve the water quality have been constructed: the EU Directives (WFD, MSFD). In respect to the implementation of the directives, many indicators are being tested and selected as powerful markers of healthy ecosystem, pollution sources that need to be monitored using sustainable and operational methods. Satellite remote sensing has become a valuable asset for monitoring water bodies and ecological status assessment. The work will focus on investigation of water quality changes in aquatic ecosystems with different trophic status and pollution gradients using Earth Observation data. Spatial focus will be given to hypereutrophic highly modified water bodies (like the Curonian Lagoon). The algal blooms will be monitored and investigated with respect of short and long-term changes of hydrophysical, hidrochemical and meteorological parameters.
Requirements for a candidate Basic knowledge of aquatic ecology and environmental sciences, experience working in the laboratory, skills in GIS methods. Candidate should be motivated to gain theoretical and practical skills on satellite data processing methods and applications. Knowledge of the English language is required.
Existing research experience A doctorate student will join the research team which has experience in the field of aquatic ecology with an application of Earth Observation data and actively collaborate with scientist from different international institutions (Italy, the Netherlands, Estonia, Sweden). This work will be implemented through the participation in the international Horizon 2020 research project (EOMORES, 2016-2019).
Existing research infrastructure Klaipeda University laboratories are well-equipped with all necessary infrastructure for samples analysis and field work. The archives of satellite data exist. Also data collected within the frame of national and international projects is available. The required licensed software is available at KU.
Potential supervisor Dr. Diana Vaičiūtė, diana.vaiciute@jmtc.ku.lt, +370 46 398877
Brief description of the topic Transitional waters are diverse, highly productive, ecologically important systems on a global scale and highly valuable for the services they provide to human societies. In turn these areas are ones of the most impacted by the global change vectors (temperature, riverine discharges, water level). The capacity to forecast the dynamics of both physical and ecological processes in these systems is of great scientific (complex interactions) and practical importance. The Harmful Algal Blooms (HABs) are typical for the transitional water ecosystems in the Northern Europe and have serious economic, ecosystem and health impacts as they produce compounds that are toxic to wildlife and humans. The ability to foresee HAB occurrence at a certain location will allow water authorities to take measures on time and reduce the risks. Work is expected to be organized around the use of 2 ecological models – one developed jointly by KU(Lithuania) and ISMAR-CNR(Italy) and second developed at Deltares (Netherlands). PhD student could have a practical placement in DELTARES and training visits to ISMAR-CNR. Models could be applied to investigate and forecast different processes as well as application of nutrient reduction technologies including so called ‘active’ or ‘living’ barrier units to improve water quality
Requirements for a candidate Good IT practical skills as well as experience in numerical modelling is expected.
Existing research experience Klaipeda University and partner organizations have international level experience in ecological model development and applications.  A number of publications derived from the output of international projects could provide a good guidance for the PhD project. This topic is linked to the FP7 INFORM and HORIZON2020 ECOPOTENTIAL projects and SBP LiveLagoons project.
Existing research infrastructure All necessary computational facilities as well as access to the databases are available.
Potential supervisor Prof. Dr. Artūras Razinkovas-Baziukas (arturas.razinkovas-baziukas@ku.lt); Prof. Georg Umgiesser (KU/ISMAR-CNR); Doc. Petras Zemlys (KU).
Potential scientific advisor Dr. Miguel Dionisio Pires (DELTARES)