Zoological Research Museum Alexander Koenig
is a member of Leibniz Association
Link to Leibniz Association
My group focuses on large-scale molecular biodiversity assessment of environmental samples, either terrestrial or aquatic habitats. Not only to identify community composition and structure but also in the long-term to establish models to predict the consequences of ecosystem changes and to pinpoint drivers of biodiversity. We use a range of molecular tools, like Next Generation Sequencing (NGS) in large-scale environmental datasets to develop approaches in a timely manner that can help to identify species/ communities but also to understand their function in ecosystem or given habitat.
The identification of taxa present in a given ecosystem is crucial to understand the ecological role of that community and therefore it is determinant for biodiversity studies. Unfortunately, biodiversity is globally decreasing and at a fast pace and thus it is fundamental to acknowledge that biodiversity contributes to ecosystem stability, resilience and function and that its loss will impact ecosystem structure and functioning and consequently humanity.
Molecular sequencing technology is advancing at a fast pace and currently it is possible to sequence a single environmental sample (bulk environmental sample) and deliver data on whole communities with even hundreds of species simultaneously. The next step in characterizing diversity and generating species lists from large-scale environmental studies is to build ecological networks, establishing the link between ecosystem structure and putative functioning. Thus the identification of ecological networks by combining current NGS technologies with bioinformatics approaches, offers a lot of potential to develop a new generation of biomonitoring tools.
“Assessing insect biodiversity along spatial and temporal dimensions in natural and agricultural areas in Brazil with NGS” (co-PI) (12,00 EUR)
“Biomonitoring diversity at the Eifel National Park using metabarcoding” GBOL2 (PI) (250,000 EUR)
“Establishing the distribution and molecular genetics of the Endangered Nimba Otter shrew (Micropotamogale lamottei) in the Putu Region of Liberia” (co-I) (8655 EUR)
“Environmental Barcoding of Aquatic Invertebrates (EBAI, MILJØ2015)”, Research Council of Norway at NTNU University Museum, Norway (Co-PI 104,850.00 EUR).
Potter C, Morgan M, Tang C, Fonseca VG, Lallias D, Gaspar J, Thomas K, Creer S (2017). De novo species delimitation in metabarcoding datasets using ecology and phylogeny (submitted).
Batista FM, Fonseca VG, Ruano F, Boudry P (2017). Asynchrony in settlement time between the closely related oysters Crassostrea angulata and C. gigas in Ria Formosa lagoon (Portugal). Marine Biology (accepted).
Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Bj.rnsd.ttir S, Boets P, Boggero A, Bones A, Borja ., Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporov.-Zatovičov. Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls ., Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot J, Fonseca V, Fontaneto D, et al. (2016) DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes 2: e11321. doi: 10.3897/rio.2.e11321
Fonseca VG & Lallias D (2016). Metabarcoding marine sediments: preparation of amplicon libraries. Methods Mol Biol. 2016;1452:183-96. doi: 10.1007/978-1-4939-3774-5_12.
Batista FM, Lopez-Sanmartin M, Boudry P, Navas JI, Ruano F, Renault T, Fonseca V, Leitao (2016). Insights on the association between somatic aneuploidy and ostreid herpesvirus 1 detection in the oysters Crassostrea gigas, C. angulata and their F1 hybrids. Aquaculture Research 47 (5), 1530-1536. doi: 10.1111/are.12613
Majaneva M, Bongard T, Diserud OH, Ekrem T, Fonseca VG, Hajibabaei M, Hob.k A, Misof B, Stur E (2015) “Environmental barcoding of aquatic invertebrates in Norway”. Genome, 2015, 58(5) doi: 163-303,10.1139/gen-2015-0087
Astrin J, Fonseca VG, Geiger M, Grobe P, Rulik B and Wagele W (2015). “Lessons from the first phase of the German Barcode of Life initiative (2012–2015)”. Genome 58(5) doi: 163-303. 10.1139/gen-2015-0087.
Felix RC, Trindade M, Pires IR, Fonseca VG, Martins RS, Silveira H, Power DM, Cardoso JC. (2015). Unravelling the Evolution of the Allatostatin-Type A, KISS and Galanin Peptide-Receptor Gene Families in Bilaterians: Insights from Anopheles Mosquitoes. PLoS One. 2015 Jul 2;10(7): e0130347. doi: 10.1371/journal.pone.0130347
Cardoso JCR, Félix RC, Martins RST, Trindade M, Fonseca VG, Fuentes J and Power DM
(2015). PACAP system evolution and its role in melanophore function in teleost fish skin.
Molecular and Cellular Endocrinology. 411:130-45. DOI: 10.1016/j.mce.2015.04.020
D Lallias, J Hiddink, VG Fonseca, J Gaspar, W Sung, SP Neill, N Barnes, T Ferrero, N Hall, PJD Lambshead, M Packer, KW Thomas and S Creer (2015). Environmental metabarcoding reveal heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. The ISME Journal doi:10.1038/ismej.2014.213.
Fonseca VG, Carvalho GR, Nichols B, Quince C, Johnson HF, Neill SP, Lambshead PJD, Thomas WK, Power DM, and Creer S. (2014). Metagenetic analysis provides new insights into the macroecology of marine meiobenthic eukaryotes. Global Ecology and Biogeography 23: 1293–1302. doi: 10.1111/geb.12223.
CR Cardoso, RC Félix, VG Fonseca and DM Power. (2012). Conservation of G-Protein Coupled Receptor (GPCR) signaling in feeding. Frontiers in Endocrinology 3: 157. doi:10.3389/fendo.2012.00157
VG Fonseca, B Nichols, D Lallias, GR Carvalho, DM Power, C Quince, & S Creer (2012). Sample richness and diversity as a driver of chimera formation in nSSU metagenetic data. Nucleic Acids Research. 40 (9): 1-9. doi:10.1093/nar/gks002
VG Fonseca, M Packer, GR Carvalho, DM Power, PJD Lambshead & S Creer (2011). Isolation of marine meiofauna from sandy sediments: from decanting to DNA extraction. Nature Protocol Exchange doi :10.1038/nprot.2010.157.
VG Fonseca, J Rosa, V Laizé, PJ Gavaia & ML Cancela (2011). Identification of a new cartilage-specific S100-like protein up-regulated during endo/perichondral mineralization in gilthead seabream. Gene Expression Patterns 11(7): 448-55. doi: 10.1016/j.gep.2011.07.003
VG Fonseca, GR Carvalho, W Sung, HF Johnson, DM Power, SP Neill, M Packer, ML Blaxter, PJD Lambshead, WK Thomas & S Creer (2010). Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications 1(7): 98. doi:10.1038/ncomms1095
S Creer*, VG Fonseca*, DL Porazinska, RM Giblin-Davis, W Sung, DM Power, GR Carvalho, ML Blaxter, PJD Lambshead & WK Thomas (2010). Ultrasequencing of the meiofaunal biosphere: practice, promises and pitfalls. Molecular Ecology 19(1): 4-20. (*joint first authors) doi: 10.1111/j.1365-294X.2009.04473.x
FM Batista, R Ben-Hamadou, VG Fonseca, N Taris, F Ruano, MA Henriques & P.Boudry (2008). Comparative study of shell shape and muscle scar pigmentation in the closely related cupped oyster taxa Crassostrea angulata, C. gigas and their reciprocal hybrids. Aquatic Living Resources 21: 31–38.
VG Fonseca*, V Laizé*, MS Valente & ML Cancela (2007). Identification of an osteopontin-like protein in fish associated with mineral formation. FEBS Journal 274: 4428-4439. (*joint first authors) DOI: 10.1111/j.1742-4658.2007.05972.x
FM Batista, A Leitão, VG Fonseca, R Ben-Hamadou, F Ruano, MA Henriques, H Guedes-Pinto, P Boudry (2007). Individual relationship between aneuploidy of gill cells and growth rate in the cupped oysters Crassostrea angulata, C. gigas and their reciprocal hybrids. Journal of Experimental Marine Biology and Ecology 352: 226–233.
FM Batista, VG Fonseca, R Ben Hamadou, N Taris, MA Henriques & P Boudry (2007). Hybridization and morphological differences between the close related oyster taxa Crassostrea angulata and C. gigas. Aquaculture 272: S244. 2017
VG Fonseca, A Lago-Lestón, V Laizé & ML Cancela (2005). Rapid identification of differentially expressed genes by in situ screening of bacteria. Molecular Biotechnology 30(2): 163-166.
VG Fonseca, N Grade & L Cancela da Fonseca (2005). Waterbird breeding on salinas in Ria Formosa, southern Portugal. Wader Study Group Bulletin 106: 58-59. (Peer Reviewed)
VG Fonseca, N Grade. & L Cancela da Fonseca (2004). Patterns of association and habitat use by migrating shorebirds on intertidal mudflats and salt works on the Tavira Estuary, Ria Formosa, southern Portugal. Wader Study Group Bulletin 105: 50–55. (Peer Reviewed)