1 Curriculum Ecology and Ethology, University of Parma. N & P

Curriculum Ecology and Ethology, University of Parma.

N & P pathways studied with network analysis in hypertrophic estuaries The Ecological Network Analysis (ENA) allows to disentangle the importance of co-occurring processes, the role of different taxa within a community, to interpret food web interactions and to compare web networks using system-level indices (Wulff et al., 1989; Borrett and Lau 2014; Christian et al. 2016; Salas and Borrett 2011; Ulanowicz and Puccia 1990). The purpose of this PhD proposal is to analyze, via combined experimental and modelling (ENA) approaches, the share of N &P fluxes among bacteria, macrofauna, primary producers, fish and birds in two hypereutrophic estuarine systems. Main aim is to address the relevance of biotic and abiotic compartments as N & P sources to macroalgae and cyanobacteria.

References Borrett, S. R., M. K. Lau. 2014. enaR: An R package for Ecosystem Network Analysis. Methods in Ecology and Evolution. 5: 1206-1213. Christian, R. R., V. F. Camacho-Ibar, M. F. Piehler, and A. R. Smyth. 2016. Improved understanding of nitrogen cycle through network models in coastal ecosystems. In: E. Wolanski and D. McLusky (chief eds.), Treatise on Estuarine and Coastal Science. Elsevier, Amsterdam, Netherlands. http://dx.doi.org/10.1016/B978-0-12-409548-9.09729-3 Salas, A. K., and S. R. Borrett. 2011. Evidence for the dominance of indirect effects in 50 trophic ecosystem networks. Ecol. Modell. 222: 1192-1204. Ulanowicz, R. E., and C. J. Puccia. 1990. Mixed trophic impacts in ecosystems. Coenoses. 5: 7-16. Wulff, F., J. G. Field, and K. H. Mann. 1989. Network Analysis in Marine Ecology: Methods and Applications. Springer-Verlag, Berlin.

Curriculum: Evolution, University of Firenze.

Compartmentalization of biosynthetic enzymes in bacterial cells This project aims at evaluating the formation of multi-enzymatic complexes (metabolons) in bacterial cells using as model systems the two metabolic pathways responsible for the biosynthesis of the aminoacids histidine and tryptophan. To this purpose a multiple experimental approach based on the utilization of genetic, biochemical and electron microscopy techniques will be used.

References 1

BRILLI, M. and FANI. R. (2004). The origin and evolution of eucaryal HIS7 genes: from metabolon to bifunctional proteins? Gene: 339, 149-160 MATHEWS, C.K., 1993. The cell-bag of enzymes or network of channels? J. Bacteriol. 175, 6377– 6381. PAPALEO M.C., RUSSO E., FONDI M., EMILIANI G., FRANDI A., BRILLI M. , PASTORELLI R,, FANI R. (2009) Structural, evolutionary and genetic analysis of the histidine biosynthetic “core” in the genus Burkholderia. Gene 448, 16-28

PEDLEY A.M. AND (2017) BENKOVIC S.J. A New View into the Regulation of Purine Metabolism: The Purinosome. Trends in Biochemical Sciences 42, 141-154 SRERE, P. (1987). Complexes of sequential metabolic enzymes. Ann Rev Bhiochem 56, 89-124

SRERE P. (2000). Macromolecular interactions: tracing the roots. Trends in Biochemical Sciences 25, 150-153

Curriculum Ecology and Ethology, University of Ferrara.

Green Infrastructures and Ecosystem Services in Anthropic and Urban spaces The candidate considering some urban ecosystems, with different geographical / environmental characteristics (plains, hills, mountains) and climatic features, but of equivalent population number and density, or the ecosystems along a gradient of urbanization, will estimate the extension of urban green areas and will evaluate their role with respect to Ecosystem Services of regulation (run -off, CO2 absorption, reduction PM10 and 2,5) and Cultural Services. The typology of present plants will be estimated and through the estimation of the LAI the gaseous exchange values will be obtained. Based on the size of the plants (height and diameter of the stem, shape and extension of the foliage) we will estimate the role in the regulation of the water cycle. Finally, Cultural Services will be estimated by giving ad hoc surveys to population samples. The results will allow to give indications of governance for the improvement of urban resilience.

References Elmqvist, T., Setälä, H., Handel, S. N., Van Der Ploeg, S., Aronson, J., Blignaut, J. N., et al. (2015). Benefits of restoring ecosystem services in urban areas. Current Opinion in Environmental Sustainability, 14, 101-108. Fusaro, L., Salvatori, E., Mereu, S., Marando, F., Scassellati, E., Abbate, G., Manes, F. (2015). Urban and peri-urban forests in the metropolitan area of Rome: Ecophysiological response of Quercus ilex

L. in two green infrastructures in an ecosystem services perspective. Urban Forestry & Urban Greening, 14(4), 1147-1156. Gómez-Baggethun, E., & Barton, D. N. (2013). Classifying and valuing ecosystem services for urban planning. Ecological Economics, 86, 235-245. Haase, D., Larondelle, N., Andersson, E., Artmann, M., Borgström, S., Breuste, J. et al. (2014). A quantitative review of urban ecosystem service assessments: concepts, models, and implementation. Ambio, 43(4), 413-433. Kremer, P., Hamstead, Z. A., McPhearson, T. (2016). The value of urban ecosystem services in New York City: A spatially explicit multicriteria analysis of landscape scale valuation scenarios. Environmental Science & Policy, 62, 57-68. Larondelle, N., & Haase, D. (2013). Urban ecosystem services assessment along a rural–urban gradient: A cross-analysis of European cities. Ecological Indicators, 29, 179-190. Livesley, S. J., McPherson, E. G., Calfapietra, C. (2016). The urban forest and ecosystem services: Impacts on urban water, heat, and pollution cycles at the tree, street, and city scale. Journal of environmental quality, 45(1), 119-124. Manes, F., Marando, F., Capotorti, G., Blasi, C., Salvatori, E., Fusaro, L., et al. (2016). Regulating Ecosystem Services of forests in ten Italian Metropolitan Cities: Air quality improvement by PM10 and O3 removal. Ecological indicators, 67, 425-440. Pappalardo, V., La Rosa, D., Campisano, A., La Greca, P. (2017). The potential of green infrastructure application in urban runoff control for land use planning: A preliminary evaluation from a southern Italy case study. Ecosystem Services, 26, 345-354. Tzoulas, K., Korpela, K., Venn, S., Yli-Pelkonen, V., Kaźmierczak, A., Niemela, J., James, P. (2007). Promoting ecosystem and human health in urban areas using Green Infrastructure: A literature review. Landscape and urban planning, 81(3), 167-178.

Curriculum: Biology and Biotechnology of plants, University of Firenze.

Taxonomic and functional diversity of the plant communities of the grasslands deserving of conservation. The proposed research would have as its object the interaction between management models and ecological theories, focusing on: 1) processes that determine the coexistence of the species in local communities, and their variation over time, including both the natural dynamic processes and the response of the species to different management models; 2) floristic, genetic and morphological-

3 functional diversity of the species that characterize these communities, and the variations induced by disturbance (eg. grazing / mowing), stress (eg. oligotrophy) or competition/exclusion effects.

References Dengler, J, Janisová, M, Török, P & Wellstein, C. 2014. Biodiversity of Palaearctic grasslands: a synthesis. Agriculture, Ecosystems and Environment 182: 1–14 Kraft, N. J., & Ackerly, D. D. (2014). Assembly of plant communities. In Ecology and the Environment (pp. 67-88). Springer New York. Grime, J.P. (1977) Evidence for the existence of three primary strategies in plants and its relevance to ecological and evolutionary theory. American Naturalist, 111, 1169–1194 Moog, D., Kahmen, S., & Poschlod, P. (2005). Application of CSR-and LHS-strategies for the distinction of differently managed grasslands. Basic and Applied Ecology, 6(2), 133-143. M. Westoby (1998) A leaf–height–seed (LHS) plant ecology strategy scheme. Plant and Soil, 199, pp. 213-227 Pierce, S., Negreiros, D., Cerabolini, B.E.L., Kattge, J., Díaz, A., Kleyer, M., Shipley B., Wright, J.S., Soudzilovskaia, N.A., (...) & Tampucci, D. 2017. A global method for calculating plant CSR ecological strategies applied across biomes world–wide. Functional Ecology 31: 444–457.

Curriculum Ecology and Ethology, University of Parma.

Behavioural ecology of the ant-fauna as a tool for the analysis of the human impact on urban biodiversity Cities are in actual fact urban ecosystems that is environments where human beings strongly interact with many other abiotic and biotic components. In this context, ants represent a group of particular interest because they are widespread and well-adapted to live in close proximity with man. Besides, they are homogeneous from a taxonomical point of view as they belong all to the same family, but at the same time they are also very diverse because species evolved a variety of adaptations promoting ant colonisation of many ecological niches. For all these reasons, ants are good candidates for the evaluation of human impact on urban biodiversity. However, more detailed studies are needed to confirm ants as a target group in this context.

References

ARONSON M.F.J., LEPCZYK C.A., EVANS K.L., GODDARD M.A., LERMAN S.B., MACIVOR J.S., NILON C.H.,

VARGO T. 2017. Biodiversity in the city: key challenges for urban green space management. Frontiers in Ecology and the Environment 15: 189–196. DOI: 10.1002/fee.1480

CERDÁ X., ARNAN X., RETANA J. 2013. Is competition a significant hallmark of ant (Hymenoptera: Formicidae) ecology? – Myrmecological News 18: 131-147.

DEL TORO I., RIBBONS R.R., PELINI S.L. 2012. The little things that run the world revisited: a review of ant-mediated ecosystem services and disservices (Hymenoptera: Formicidae). – Myrmecological News 17: 133-146.

ELMQVIST T., SETÄLÄ H., HANDEL S.N., VAN DER PLOEG S, ARONSON J., BLIGNAUT J.N., GOMEZ-

BAGGETHUN E., NOWAK DJ, KRONENBERG J., DE GROOT R. 2015. Benefits of restoring ecosystem services in urban areas. – Current Opinion in Environmental Sustainability 2015, 14:101–108. DOI: 10.1016/j.cosust.2015.05.001

GUENARD B., CARDINAL-DE CASAS A., DUNN R. R. 2015. High diversity in an urban habitat: are some animal assemblages resilient to long-term anthropogenic change? Urban Ecosystems, 18(2), 449- 463. DOI 10.1007/s11252-014-0406-8

KOWARIK I. 2011. Novel urban ecosystems, biodiversity, and conservation. – Environmental Pollution 159: 1974-1983. DOI: 10.1016/j.envpol.2011.02.022

MENKE S.B., GUÉNARD B., SEXTON J., SILVERMAN J., DUNN R.R. 2011. Urban areas may serve as habitat and corridors for dry-adapted, heat tolerant species; an example from ants. – Urban Ecosystems 14: 135-163. DOI 10.1007/s11252-010-0150-7

NEW T. M. 2018. Promoting and developing insect conservation in Australia’s urban environments. – Austral Entomology. DOI: 10.1111/aen.12332

PEĆAREVIĆ M., DANOFF-BURG J., DUNN R. R. 2010. Biodiversity on Broadway - Enigmatic Diversity of the Societies of Ants (Formicidae) on the Streets of New York City. – Plos One 5: e13222. DOI: 10.1371/journal.pone.0013222

PENICK C. A., SAVAGE A.M., DUNN R. R. 2015. Stable isotopes reveal links between human food inputs and urban ant diets. – Proceedings of the Royal Society B 282. DOI: 10.1098/rspb.2014.2608

SANTOS M.N. 2016. Research on urban ants: approaches and gaps. – Insectes Sociaux 63: 359–371. DOI 10.1007/s00040-016-0483-1

SCHWARZ N., MORETTI M., BUGAHLO M.N., DAVIES Z.G., HAASE D., HACK J., HOF A., MELERO Y., PETT

T.J., KNAPP S. 2017. Understanding biodiversity-ecosystem service relationships in urban areas: A comprehensive literature review. – Ecosystem Services 27: 161–171. DOI: 10.1016/j.ecoser.2017.08.014

Curriculum Biology and Biotechnology of plants, University of Ferrara.

Variations of thylakoid organization in plant organisms differing in their phylogenetic position. The candidate will deal with the variations induced by different environmental factors (in particular quality and quantity of light) on the organization of the photosynthetic membranes, with emphasis on the supramolecular interactions of photosystems. The study includes the comparison of responses in phylogenetically divergent organisms, such as green algae, diatoms, pteridophytes, spermatophytes. Methods applied for the study are: microscopic and ultramicroscopic, biochemical and biophysical analyses.

References Katalin Solymosi. Plastid Structure, Diversification and Interconversions I. Algae. Current Chemical Biology, 2012, 6, 167-186 Katalin Solymosi and Áron Keresztes . Plastid Structure, Diversification and Interconversions II. Land Plants. Current Chemical Biology, 2012, 6, 187-204 Martina Giovanardi, Mariachiara Poggioli, Lorenzo Ferroni, Maija Lespinasse, Costanza Baldisserotto, Eva-Mari Aro, Simonetta Pancaldi. Higher packing of thylakoid complexes ensures a preserved Photosystem II activity in mixotrophic Neochloris oleoabundans. Algal Research, 25, 2017, 25, 322-332 Irina Grouneva, Peter J. Gollan, Saijaliisa Kangasjarvi, Marjaana Suorsa, Mikko Tikkanen, Eva-Mari Aro. Phylogenetic viewpoints on regulation of light harvesting and electron transport in eukaryotic photosynthetic organisms. Planta, 2013, 237, 399–412 Reinat Nevo, Dana Charuvi, Onie Tsabari and Ziv Reich. Composition, architecture and dynamics of the photosynthetic apparatus in higher plants. The Plant Journal, 2012, 70, 157–176 Mathias Pribil, Mathias Labs and Dario Leister. Structure and dynamics of thylakoids in land plants. Journal of Experimental Botany Advance Access published March 12, 2014. doi:10.1093/jxb/eru090 Jan M. Anderson1, Peter Horton, Eun-Ha Kim, and Wah Soon Chow. Towards elucidation of dynamic structural changes of plant thylakoid architecture. Phil. Trans. R. Soc. B, 2012, 367, 3515– 3524 Roman Kouril, Lukas Nosek, Jan Bartos, Egbert J. Boekema and Petr Ilık. Evolutionary loss of light- harvesting proteins Lhcb6 and Lhcb3 in major land plant groups – break-up of current dogma. New Phytologist (2016) doi: 10.1111/nph.13947

Tobias Schumann, Suman Paul, Michael Melzer, Peter Dörmann and Peter Jahns. Plant Growth under Natural Light Conditions Provides Highly Flexible Short-Term Acclimation Properties toward High Light Stress. Front. Plant Sci. 8:681. doi: 10.3389/fpls.2017.00681 Marjaana Rantala, Mikko Tikkanen and Eva-Mari Aro. Proteomic characterization of hierarchical megacomplex formation in Arabidopsis thylakoid membrane. The Plant Journal, 2017, 92, 951–962

Curriculum Biology and Biotechnology of plants, University of Parma.

Plant-pathogen interaction: bacterial photoreceptor role in virulence and plant disease resistance in the system Pseudomonas syringae pv. tomato-tomato Aim of the research project is to study the role of bacterial photoreceptors during the plant-pathogen interaction in the patho-system Pseudomonas syringae pv. tomato DC3000-tomato. Wild-type and bacterial strains lacking the genes for the bacterial photoreceptors will be used in the experiments. Moreover, tomato plant disease symptoms and/or immune response will be analysed after the infection with the different bacterial strains.

References McGrane R, Beattie GA (2017) Pseudomonas syringae pv. syringae B728a regulates multiple stages of plant colonization via the bacteriophytochrome BphP1. mBio 8:e01178-17. https://doi.org/10.1128/mBio.01178-17 Losi, A, Gärtner W (2017) Solving blue light riddles: new lessons from flavin-binding LOV photoreceptors. Photochemistry and photobiology 93: 141-158 Ricci A, Dramis L, Shah R, Gärtner W, Losi A (2015) Visualizing the relevance of bacterial blue- and red-light receptors during plant-pathogen interaction. Environmental Microbiology Reports 7(5): 795-802 Trdá L, Boutrot F, Claverie J, Brulé D, Dorey S and Poinssot B (2015) Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline. Front. Plant Sci. 6: 219. doi: 10.3389/fpls.2015.00219 Kumar D (2014). Salicylic acid signaling in disease resistance. Plant Science 228: 127-134 Losi A, Mandalari C, Wolfgang Gärtner W (2014) From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World. Plants 3: 70-94 Ichinose Y, Taguchi F, Mukaihara T (2013) Pathogenicity and virulence factors of Pseudomonas syringae. J Gen Plant Pathol 79: 285-296

Wu L, McGrane RS, Beattie GA (2013) Light regulation of swarming motility in Pseudomonas syringae integrates signaling pathways mediated by a bacteriophytochrome and a LOV protein. mBio 4(3):e00334-13. doi:10.1128/mBio.00334-13. Islam S, Babadoost M, Bekal S, Lambert K (2008) Red light-induced systemic disease resistance against root-knot nematode Meloidogyne javanica and Pseudomonas syringae pv. tomato DC 3000. J. Phytopathology 156: 708-714 Melotto M, Underwood W, He S (2008) Role of stomata in plant innate immunity and foliar bacterial diseases. Annu. Rev. Phytopathol. 46: 101-22

Curriculum Ecology and Ethology, University of Firenze.

The role of ants in ecosystem dynamics: trophic interactions, competition, and nutrient cycling. The project aims to analyze the interactions between ants and the biotic and abiotic components of model ecosystems. In particular, we will address: i) trophic interactions, ii) competition among ants and between these and other arthropods; iii) mutualism; iv) effects of ants on nutrient cycling. The research will be carried out using a combination of experiments and observations both in the field and the lab and will use advanced techniques for the identification of trophic relationship (e.g. Stable Isotopes Analysis).

References Blüthgen N., Gebauer G., Fiedler K. (2003). Disentangling a rainforest food web using stable isotopes: dietary diversity in a species-rich ant community. Oecologia 137(3): 426-435. Brewitt K., Piñol J., Werner C., Beyschlag W., Espadaler X., Hidalgo N. P., Platner C.(2015). Evaluating the importance of trophobiosis in a Mediterranean ant community: a stable isotope analysis. Insectes sociaux 62(1): 81-95. Gibb H. & Cunningham S. A. (2011). Habitat contrasts reveal a shift in the trophic position of ant assemblages. Journal of Animal Ecology 80(1): 119-127. Hawes C., Stewart A., Evans H. (2002). The impact of wood ants (Formica rufa) on the distribution and abundance of ground beetles (Coleoptera: Carabidae) in a Scots pine plantation. Oecologia 131(4): 612-619. Iakovlev I. K., Novgorodova T. A., Tiunov A. V., Reznikova Z. I. (2017). Trophic position and seasonal changes in the diet of the red wood ant Formica aquilonia as indicated by stable isotope analysis. Ecological Entomology 42(3): 263-272. 8

Jílková V., Pîcek T., Šestauberová , Krištůfek V., Cajthaml T., Frouz J. (2016) Methane and carbon dioxide flux in the profile of wood ant (Formica aquilonia) nests and the surrounding forest floor during a laboratory incubation FEMS Microbiology Ecology 92 Laakso J. (1999). Short-term effects of wood ants (Formica aquilonia Yarr.) on soil animal community structure. Soil biology and biochemistry 31(3): 337-343. Parmentier T., Bouillon S., Dekoninck W., Wenseleers T. (2016). Trophic interactions in an ant nest microcosm: a combined experimental and stable isotope (δ 13 C/δ 15 N) approach. Oikos 125(8): 1182-1192. Platner C., Piñol J., Sanders D., Espadaler X. (2012). Trophic diversity in a Mediterranean food web— Stable isotope analysis of an ant community of an organic citrus grove. Basic and applied ecology 13(7): 587-596. Tillberg C. V., Holway D. A., LeBrun E. G., Suarez A. V. (2007). Trophic ecology of invasive Argentine ants in their native and introduced ranges. Proceedings of the National Academy of Sciences 104(52): 20856-20861.

Curriculum: Evolution. University of Ferrara.

Metagenomic analysis of subgingival microbiota of diabetics and non-diabetics with different periodontal conditions The PhD project aims to explore the genomic component of oral microbiome (metagenome) and its relationship to the genetic host factors determining susceptibility to Type 2 Diabetes (T2D), with and without concomitant Periodontitis (P). The relationship between P and T2D is well known and several recent studies showed how the microbial profile changes in enterotypes composition has a high relevance in diagnosis and management of the diseases. However, the recent NGS approaches have questioned the oral microbial profile outlined to date. The primary objective of the project will be the characterization by whole metagenomic shotgun of the oral microbiome of T2D, P and healthy subjects. The taxonomic assignment, the de novo assembly of the main observed enterotypes and the related functional annotation that will serve for an effective understanding of the biological and evolutionary processes of the microbial communities that reside in the oral cavity.

References Casarin RC, Barbagallo A, Meulman T, et al. Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis. J Periodontal Res 2013; 48: 30-36.

Babaev EA, Balmasova IP, Mkrtumyan AM, et al. Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus. Bull Exp Biol Med 2017; 163: 718-721. Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. (2017) Shotgun metagenomics, from sampling to analysis. Nature biotechnology, 35: 833-844; Siqueira JF Jr, Rôças IN. (2017) The Oral Microbiota in Health and Disease: An Overview of Molecular Findings. Methods Mol Biol. 1537:127-138 Human Microbiome Project Consortium. (2012) A framework for human microbiome research. Nature. Jun 13;486(7402):215-21 Wang J, Qi J, Zhao H, et al. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Scientific reports 2013; 3: 1843. Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE (2014) Conducting a microbiome study. Cell 17;158(2):250-262. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S. (2012) Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919. Ai D, Huang R, Wen J, Li C, Zhu J, Xia LC. (2017) Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics. 2017 Jan 25;18(Suppl 1):1041. doi: 10.1186/s12864-016-3254-5. Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL. (2016) Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun. 2016; 469(4):967-77