Professor Si Creer

Professor Si Creer
Name
Professor Si Creer
Position
Professor of Molecular Ecology
Email
s.creer@bangor.ac.uk
Phone
+44 1248 382302
Location
School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK

About

I am interested in using contemporary molecular tools to address diverse questions focusing on biodiversity, ecology and evolution. This is a particularly exciting time in the field of molecular ecology, since advances in DNA sequencing throughput have recently offered a paradigm shift in our ability to assess previously intractable functional and taxonomic biodiversity at an unprecedented scale, augmenting existing biodiversity fields and empowering others. Using such technologies, I am testing a range of hypotheses regarding the alpha and beta functional and taxonomic diversity of macro-, meio- and microbial communities (e.g. microbiomes) in space and time, based on genomic, community and environmental DNA (eDNA). Focal habitats have included estuarine, coastal and deep sea environments with an increasing focus now on freshwater, terrestrial, whole organisms and the aerial biosphere in order to understand the drivers of diversity in natural communities and also how diversity is linked with ecological function, trophic relationships, environmental and human health. Current additional activities include phylogenomics, population genetics, life history evolution, polyploidy, pollination genomics. If you want to find out more, please go to my research and publication pages.

If you are interested in this sort of work or life, please follow me on Twitter: @spideycreer

Recent Methods in Ecology and Evolution podcast on the use of DNA sequencing to identify biodiversity (Creer et al. MEE 2016) also available here.

CV

Education

  • 2005 Teaching in Higher Education Certificate. UWB.
  • 2000 PhD. Molecular phylogeography and venom evolution of Trimeresurus stejnegeri in Taiwan. NERC funded, The University of Wales, Bangor (UWB), UK.
  • 1997 MSc. Ecology (Distinction). NERC funded, UWB.
  • 1992 BSc. (Hons) Applied Biology (2.1). University of Bath, UK.

Career

  • 9/16 – Professor of Molecular Ecology – Bangor University.
  • 11/12–9/16 – Senior Lecturer in Molecular Ecology – Bangor University.
  • 11/05–10/11 Senior Research Fellow in Molecular Ecology – Bangor University.
  • 07/05–10/05 Postdoctoral Research Associate. NERC grant, “Functional and genomic venom diversity of phospholipase A2 (PLA2) genes in Asian pitvipers” UWB.
  • 06/01–06/05 Postdoctoral Research Associate (named). Wellcome Trust grant, “Reliable molecular phylogenies for medically important venomous snakes: subtropical and tropical Asian vipers” UWB.
  • 09/03–09/04 Temporary Lectureship in Zoology. UWB.
  • 01–06/01 Postdoctoral Research Associate. Leverhulme Trust grant, “Far-east Asian pitvipers: venom evolution and biodiversity” University of Wales, Bangor.

Grants and Awards

  • 2016–2019 NERC Standard Grant (PI) – PollerGEN – Using molecular genetics to understand grass species pollen deposition: enhancing bio-aerosol models and implications for human health (£1.2M, with Natasha DeVere, Gareth Griffith, Matt Hegarty, Aberystwyth; Carsten Skjøth, Worcester; Nick Osborne and Ben Wheeler, Exeter and the UK Met Office)
  • 2015–2020 NERC Highlight Topic Grant (PI) – Understanding the ecological relevance of eDNA in freshwater lotic ecosystems (LOFRESH: £1.25M, with Mark DeBruyn, Gary Carvalho; CEH Bangor; John Colbourne, Holly Bik, Birmingham and Isabelle Durance and Steve Ormerod, Cardiff)
  • 2015–2020 NERC Large Grant (CoI) – Impacts of global warming in sentinel systems: from genes to ecosystems (£3.7M, with Guy Woodward, Imperial)
  • 2015–2017 Marie Curie Intra-European Fellowship (CoI) with Laura Kelly – PARMIN (£200K)
  • 2014–2016 Royalty Research Fund Small Grant, University of Washington (CoI) with Lorenz Hauser – Tackling the meiofauna paradox with metagenetics ($40K)
  • 2014–2016 Formas, Sweden (CoI) – 2 year mobility grant with Francisco Nascimento (£150K)
  • 2016–2017 Vetenskapsrådet (VR) (CoI) One year postdoc grant with Francisco Nascimento (£31K)
  • 2014–2015 SciLifeLab (CoI) – National projects in Swedish Genomes and Biodiversity with Francisco Nascimento (£15K)
  • 2013–2016 Welsh Government Grant (CoI) – Glastir Monitoring and Evaluation Programme (GMEP): Soil biodiversity (£4M, with CEH and GMEP Consortium)
  • 2013–2015 AQUATRACE: Linking life-history traits and genetic variation (Co-I) in collaboration with Einar Nielsen DTU-Aqua Denmark (168K Euros)
  • 2012–2015 – FISHPROBIO (PI) : Marie Curie Outgoing Fellowship with Martin Llewelyn (290,000 Euros)
  • 2011–2013 National Science Centre (Poland) (CoI) – Seasonal differences in diversity of bacteria and pico- and nanoplanktonic protists in 3 zones of the Vistula River estuary (£121K)
  • 2010–2011 – NERC AFI (PI) Collaborative Gearing Scheme grant: A second-generation sequencing perspective of the Antarctic bentho-pelagic microbial biosphere
  • 2010–2012 – MARMEDIV (PI) : Marie Curie Incoming Fellowship with Frederic Sinniger (174,000 Euros)
  • 2009 - Natural Environment Research Council (NERC) (PI) Environmental genomics of life in the intertidal: Design and optimization of a gastropod microarray (£8000)
  • 2008–2010- NERC (PI)Post genomic and proteomics grant: Sequencing the meiofaunal metagenome of the marine/freshwater interface in key estuarine ecosystems (£140000)
  • 2008- CoSyst (PI) : The Systematics Association, The Linnean Society, Biotechnology and Biological Sciences Research Council (BBSRC), NERC: Advancing mitogenomics via ultrasequencing: A case study within the Araneae (£10200)
  • 2007 – NERC (PI) Phylochip development for the rapid identification of littoral meiofaunal communities (£4750)
  • 2006–2009 – NERC (PI) New Investigator Award (PI) : Are marine nematodes hyperdiverse? A metagenomic solution (£76000)
  • 2004 Joseph B. Slowinski Award for the most distinguished international paper on snake systematics for Creer et al (2003a) ($500)
  • 1997 UWB Llewellyn and Mary Williams Scholarship for PhD funding (£14000)
  • 1996 NERC MSc funding (£3500)

Professional Activities

In addition to the above, I review articles for Nature Communications, Systematic Biology, Molecular Ecology, Philosophical Transactions and Proceedings of the Royal Society, Biological Sciences, BMC Evolutionary Biology, Conservation Genetics, Heredity, Journal of Molecular Evolution, Journal of Experimental Marine Biology and Ecology, Journal of Fish Biology, Journal of Zoology, Environmental Microbiology and Marine Ecology Progress Series.

Research

Research interests

LOFRESH – Understanding the ecological relevance of lotic environmental DNA (eDNA)

In recent years, paradigm shifts have been made in using DNA sourced directly from environmental samples (eDNA), to identify large-scale patterns of biodiversity from taxa across the tree of life. LOFRESH is a multi-institution collaborative initiative funded by a Natural Environment Research Council (NERC) Highlight Topic grant to improve our ability to utilize eDNA for tracking the presence and abundance of species in and around freshwater habitats. Environmental DNA refers to shed cells or extracellular DNA from organisms as they pass through an environment (e.g. water, soil and air), or die and decay. By doing so, animals and plants leave traces of their DNA in the environment that can be detected using a number of molecular genetic approaches.

We expect that our findings will provide valuable insights for the fields of freshwater ecology, biomonitoring and environmental assessment. Launched in March 2016, LOFRESH aims to understand the dynamics between living communities and lotic (i.e. riverine) eDNA in relation to spatial and environmental variation.

While led by Bangor University, LOFRESH is also directly supported by The Centre for Ecology and Hydrology (CEH), Cardiff University and the University of Birmingham. Please visit the project website for further details and please do get in touch if you would like to explore future synergies with the project, or associated research areas.

NERC PollerGEN – Understanding links between grass pollen and human health in the UK

For millions of people, the onset of spring and summer brings misery as they battle with itchy eyes and sneezing brought about by their reaction to pollen. Up to 25% of the UK population are sensitised to grass pollen and around 10% suffer asthma that can be aggravated by pollen. However, with around 150 different species of grass in the UK and no easy way of distinguishing between different pollen grains, identifying which species of grass pollen people are allergic to is a challenge.

In PollerGEN, a £1.2M NERC investment, we aim to develop a species level, spatio-temporal pollen assessment framework throughout the UK and develop novel pollen bio-aerosol models in order to identify which species are linked to the exacerbation of asthma.

The PollerGEN team comprises researchers from Bangor, Aberystwyth, Worcester and Exeter Universities, in collaboration with the UK Met office, supported by a range of stakeholder groups and charities. We will use a range of molecular genetic solutions, from shotgun environmental sequencing through to quantitative PCR to quantify the pollen landscape, followed by leading-edge aerobiological modelling and identifying links to the aggravation of asthma throughout the grass pollen season.

Understanding which species of grass pollens are in the air in high quantities at a particular time will allow those with hay fever and asthma to better manage their disease by being aware of risky periods, avoiding exposure and having their medicines to hand. It is predicted that the new forecasts will give more precise (and shorter) time periods that disease sufferers will have to be cautious in, and provide guidance of when these may occur.

Enhancing freshwater ecosystem biomonitoring: defining and testing an ecometagenetic DNA identification framework.

Biological indicators are used to estimate the state of the environment and the Environment Agency mandatorily monitors the health of freshwater ecosystems throughout the UK. However, traditional monitoring approaches suffer from the “identification bottleneck” problem (e.g. subjectivity, lack of resolution, labour-intensive traditional taxonomy approaches mismatched with ecosystem diversity). This KESS-funded PhD program, in collaboration with Iliana Bista and the Environment Agency, will populate a DNA reference library for up to 200 macroinvertebrate indicator species and test and test the efficacy of the use of second generation sequencing approaches in enhancing freshwater biomonitoring programs. Chironomid image ©entomart.

Understanding the microbial mechanisms underpinning carbon release from peatland ecosystems.

In their natural waterlogged state, peatlands constitute the most important, long-term, terrestrial organic carbon store on our planet. However, it has been shown that under drought conditions the stored carbon is released as atmospheric gaseous CO2 and dissolved organic carbon (DOC) into surrounding waterways, contributing to global warming and the net loss of carbon from peatland ecosystems. Here, funded by the HPC Wales/Fujitsu partnership and partnered with Welsh Water, we will use “metagenetic” and shotgun “metagenomic” approaches to identify both the composition and functional diversity of the microbial communities responsible for drought-driven carbon loss from a range of peatland ecosystems. By understanding the mechanisms associated with carbon loss, we will be able to explore approaches aimed at regulation of key microbial drivers of carbon loss through the geo-engineering of peatlands to regain carbon. Such a multidisciplinary project demands expertise in wetland biogeochemistry and metagenomics and is lead by Caitlin Potter, in collaboration with Prof. Chris Freeman, Prof. Peter Golyshin, Dr. Nathalie Fenner and Dr. James McDonald.

Glastir Monitoring and Evaluation Programme (GMEP): Soil biodiversity

Intensively monitoring ecosystems in relation to land management schemes and monitoring progress towards a range of international biodiversity and environmental targets is a crucial aspect of understanding landscape interventions and the effects of environmental change. As part of the wider Glastir Monitoring and Evaluation Programme (GMEP), this project will investigate alpha and beta diversity of soil prokaryote, fungal and microbial eukaryotes and a range of abiotic soil factors across the Welsh landscape. Our aim is to better understand linkages and drivers of biodiversity between the abiotic and biotic realms and potential linkages between below-ground and above ground processes in relation to management regimes employed across a variety of ecological habitats.

Click here to view the Past Research Projects.

Publications

2019

2018

2017

  • PublishedEvaluation of mesofauna communities as soil quality indicators in a national-level monitoring programme
    George, P., Keith, A. M., Creer, S., Barrett, G. L., Lebron, I., Emmett, B. A., Robinson, D. & Jones, D., 1 Dec 2017, In : Soil Biology and Biochemistry. 115, p. 537-546
    Research output: Contribution to journalArticle
  • PublishedJellyfish on the menu: mtaDNA assay reveals scyphozoan predation in the Irish Sea
    Lamb, P. D., Hunter, E., Pinnegar, J. K., Creer, S., Davies, R. G. & Taylor, M. I., 29 Nov 2017, In : Royal Society Open Science.
    Research output: Contribution to journalArticle
  • PublishedA communal catalogue reveals Earth's multiscale microbial diversity
    Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vazquez-Baeza, Y., Gonzalez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Song, S. J., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., Knight, R., Agosto Rivera, J. L., Al-Moosawi, L., Alverdy, J., Amato, K. R., Andras, J., Angenent, L. T., Antonopoulos, D. A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J. K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J. F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D. M., Braun, J., Brazelton, W., Brearley, F. Q., Campbell, A. H., Caporaso, J. G., Cardona, C., Carroll, J., Cary, S. C., Casper, B. B., Charles, T. C., Chu, H., Claar, D. C., Clark, R. G., Clayton, J. B., Clemente, J. C., Cochran, A., Coleman, M. L., Collins, G., Colwel, R. R., Contreras, M., Crary, B. B., Creer, S., Cristol, D. A., Crump, B. C., Cui, D., Daly, S. E., Davalos, L., Dawson, R. D., Defazio, J., Delsuc, F., Dionisi, H. M., Dominguez-Bello, M. G., Dowell, R., Dubinsky, E. A., Dunn, P. O., Ercolini, D., Espinoza, R. E., Ezenwa, V., Fenner, N., Findlay, H. S., Fleming, I. D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E. S., Galindo, G., Garcia, L., Garcia-Amado, M. A., Garshelis, D., Gasser, R. B., Gerdts, G., Gibson, M. K., Gifford, I., Gill, R. T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H-P., Guyton, K., Haig, S-J., Hale, V., Hall, R. S., Hallam, S. J., Handley, K. M., Hasan, N. A., Haydon, S. R., Hickman, J. E., Hidalgo, G., Hofmockel, K. S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J. D., Jastrow, J. D., Jex, A. R., Johnson, L. S., Johnston, E. R., Joseph, S., Jurburg, S. D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C. T. E., Kennedy, S. J., Kerkhof, L. J., King, G. M., Kling, G. W., Koehler, A. V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E. M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I. I., Liancourt, P., Liang, W., Linz, A. M., Lipson, D. A., Liu, Y., Lladser, M. E., Lozada, M., Spirito, C. M., MacCormack, W. P., MacRae-Crerar, A., Magris, M., Martín-Platero, A. M., Martín-Vivaldi, M., Martínez, L. M., Martínez-Bueno, M., Marzinelli, E. M., Mason, O. U., Mayer, G. D., McDevitt-Irwin, J. M., McDonald, J., McGuire, K. L., McMahon, K. D., McMinds, R., Medina, M., Mendelson, J. R., Metcalf, J. L., Meyer, F., Michelangeli, F., Miller, K., Mills, D. A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R. M., Munroe, P., Myrold, D., Neufeld, J. D., Ni, Y., Nicol, G. W., Nielsen, S., Nissimov, J. I., Niu, K., Nolan, M. J., Noyce, K., O’Brien, S. L., Okamoto, N., Orlando, L., Ortiz Castellano, Y., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J. M., Petraitis, P., Pfister, C., Pilon-Smits, E., Piombino, P., Pointing, S. B., Pollock, F. J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A. P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K. J., Rodriguezl, S. M., Rohwer, F., Roundstone, W., Safran, R. J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M. D., Scott, N. M., Seger, R. L., Seguin-Orlando, A., Seldin, L., Seyler, L. M., Shakhsheer, B., Sheets, G. M., Shen, C., Shi, Y., Shin, H., Shogan, B. D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D. P., Soler, J. J., Sperling, M., Steinberg, P. D., Stephens, B., Stevens, M. A., Taghavi, S., Tai, V., Tait, K., Tan, C. L., Tas, N., Taylor, D. L., Thomas, T., Timling, I., Turner, B. L., Urich, T., Ursell, L. K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Vega Thurber, R., Vitaglione, P., Walker, D. A., Walters, W. A., Wang, S., Wang, T., Weave, T., Webster, N. S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J. J., West, K., Whitehead, A., Whitehead, S. R., Whittingham, L. A., Willerslev, E., Williams, A. E., Wood, S. A., Woodhams, D. C., Yang, Y., Zaneveld, J., Zarraonaindia, I., Zhang, Q. & Zhao, H., 23 Nov 2017, In : Nature. 551, 7681, p. 457-+
    Research output: Contribution to journalArticle
  • PublishedEnvironmental DNA metabarcoding: transforming how we survey animal and plant communities
    Deiner, K., Bik, H. M., Machler, E., Seymour, M., Lacoursiere-Roussel, A., Altermatt, F., Creer, S., Bista, I. & Lodge, D. M., Nov 2017, In : Molecular Ecology Resources. 26, 21, p. 5872-5895
    Research output: Contribution to journalArticle
  • PublishedSubtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems
    Potter, C., Freeman, C., Golyshin, P., Ackerman, G., Fenner, N., McDonald, J., Ehbair, A., Jones, T., Murphy, L. & Creer, S., Sep 2017, In : Scientific Reports. 7, 11314.
    Research output: Contribution to journalArticle
  • PublishedRevealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach
    Fonseca, V. G., Sinninger, F., Gaspar, J. M., Quince, C., Creer, S., Power, D., Peck, L. S. & Clark, M. S., 21 Jul 2017, In : Scientific Reports. 7, 6094.
    Research output: Contribution to journalArticle
  • PublishedTideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: the case study of the Vistula river estuary
    Golebiewski, M., Calkiewicz, J., Creer, S. & Piwosz, K., Apr 2017, In : Environmental Microbiology Reports. 9, 2, p. 129-143
    Research output: Contribution to journalArticle
  • PublishedAnnual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity
    Bista, I., Carvalho, G., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M. & Creer, S., Jan 2017, In : Nature Communications. 8, 14087.
    Research output: Contribution to journalArticle
  • PublishedParasitism perturbs the mucosal microbiome of Atlantic Salmon
    Llewellyn, M. S., Leadbeater, S., Garcia, C., Sylvain, F-E., Custodio, M., Ang, K. P., Powell, F., Carvalho, G., Creer, S., Elliot, J. & Derome, N., 2017, In : Scientific Reports. 7, 43465.
    Research output: Contribution to journalArticle
  • PublishedUsing DNA metabarcoding to investigate honey bee foraging reveals limited flower use despite high floral availability
    De Vere, N., Jones, L. E., Gilmore, T., Moscrop, J., Lowe, A., Smith, D., Hegarty, M. J., Creer, S. & Ford, C. R., 2017, In : Scientific Reports. 7, 42838.
    Research output: Contribution to journalArticle

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