Caring about the future

Daniel Cleary

Daniel Cleary

Principal Researcher (Research Career)

  • Author Name : Cleary DFR

  • Researcher ID: D-2582-2012
  • ORCID: 0000-0002-6143-3390
  • Ciencia ID: EB10-9E4E-5642
  • Department: Biology
  • Research Group: Coastal and Deep-Ocean Ecology & Conservation (CDEC)
  • ISI Web of KnowledgeSM search factor: AU=(Cleary DFR)

Research interests

As CESAM researcher I played a key role in helping to establish LEMAM, which houses a state-of-the art laboratory and an experimental microcosm system, described in the journal Global Change Biology. This was the first in a series of publications in high impact journals where the impact of climate change on sediment microbial communities was assessed.

I have been also involved in a range of other research projects including studies of microbial communities associated with various coral reef organisms and identifying the potential roles and functions of microbial communities in aquaculture systems.

I like generating and analysing large data sets, for example, using next generation sequencing. This has played a key role in maintaining my scientific output.

Academic degrees

Ph.D. in Biology. Institute of Biodiversity and Ecosystem Dynamics – University of Amsterdam (2002).

Masters in Biology. Institute of Biodiversity and Ecosystem Dynamics – University of Amsterdam (1993).

Scientific activities

Principal Researcher at the Centre for Environmental and Marine Studies (CESAM) and Department of Biology (DeBio) of the University of Aveiro, Portugal (2013 - present).

Coordinating Researcher of the Laboratory of Molecular Studies for Marine Environments (LEMAM), University of Aveiro, Portugal (2009 – present).

Assistent researcher, CESAM and University of Aveiro (2008 - 2013)

Postdoctoral researcher, University of Amsterdam (2006 - 2008)

Postdoctoral researcher, Naturalis Biodiversity Center (2003 - 2006)

Postdoctoral researcher, University of Amsterdam (2002 - 2003)

PhD student, University of Amsterdam (1997 - 2002)

Research assistant, University of Amsterdam (1995 - 1996)


Key Recent Publications

Oliveira V., Polónia A.R.M, Cleary D.F.R., Yusheng M.A., de Voogd N.J., Rocha U.N., Gomes N.C.M. (2020) Characterization of putative circular plasmids in sponge‐associated bacterial communities using a selective multiply‐primed rolling circle amplification. Molecular Ecology Resources. (IF 6.28)

Cleary DFR, Polónia ARM, Huang YM, Gomes NCM, de Voogd NJ. 2019. A comparison of prokaryote communities inhabiting sponges, bacterial mats, sediment and seawater in Southeast Asian coral reefs. FEMS Microbiology Ecology 95: fiz169. Doi: 10.1093/femsec/fiz169.

Cleary DFR, Swierts T, Coelho FJRC, Polónia ARM, Huang YM, Ferreira MRS, Putchakarn S, Carvalheiro L, van der Ent E, Ueng JP, Gomes NCM, de Voogd NJ. 2019. The sponge microbiome within the greater coral reef microbial metacommunity. Nature Communications 10: 1644. DOI: 10.1038/s41467-019-09537-8.

Swierts T, Cleary DFR, de Voogd NJ. 2018. Biogeography of prokaryote communities in closely related giant barrel sponges across the Indo-Pacific. FEMS Microbiol Ecol. 94(12): fiy194. DOI: 10.1093/femsec/fiy194.

Cleary DFR, Polónia ARM, de Voogd NJ. 2018. Bacterial communities inhabiting the sponge Biemna fortis, sediment and water in marine lakes and the open sea. Microbial Ecology 76: 610-624. DOI: 10.1007/s00248-018-1156-6.

Cleary DFR, Polónia ARM, de Voogd NJ. 2018. A comparison of Prokaryote community composition in two Cinachyrella morphospecies and water from west Papuan marine lakes. FEMS Microbiology Ecology 94(2): fix175. doi: 10.1093/femsec/fix175.



BlueComposite See more

MicroNiche – Exploring the endolithic niche of coral symbiotic microalgae inside reef sand grains See more

MAXIMUS.PT - Research and development for the production of larvae and juveniles of turbot in maternity See more

4D-REEF-Past, present, and future of coral reefs in the Coral Triangle See more

Symbioreactor - Sustainable Production of Bioactive Metabolites from Microbial Symbionts of Marine Sponges and Corals See more

STEP - Integrated System for Managing Fishfarm Effluents See more

LTER-RAVE - Long term monitoring in the Ria de Aveiro: towards a deeper understanding of ecological, environmental and economic processes See more

LAGOONS - Integrated water resources and coastal zone management in European lagoons in the context of climate change See more

AQUASAFE - Development of new technologies to anticipate and diagnose disease outbreaks in aquaculture See more

RASTREMAR - Use of molecular tools in the traceability of marine food products See more

LESS CORAL: The impact of human settlLEmentS on CORAL reef ecosystems See more

DiverseShores - Testing associations between genetic and community diversity in European rocky shore environments See more

DOMINO EFFECT - Degradation of lOtic ecosysteMs assocIated with plaNtation fOrestry: An Evaluation of plantation Forest Food-wEb CommuniTies See more

Global climate change and pollution: a synergy designed for disaster? See more

Scientific Supervision

Master (Main Supervisor): Dille Wielakker (not a CESAM member)

Master (Main Supervisor): Annemieke Bijlmer (not a CESAM member)

Master (Main Supervisor): Andreia Gonçalves Sousa (not a CESAM member)

Master (Main Supervisor): Ana Cecília da Cruz Pires (ex-CESAM member)

Master (Main Supervisor): Lisa Becking (not a CESAM member)

Master (Main Supervisor): Paola Rachello-Dolmen (not a CESAM member)

Master (Co-supervisor): Pedro Miguel Pinheiro Saraiva (not a CESAM member)

Master (Co-supervisor): Gomes, Hélder Alexandre Campos (ex-CESAM member)

PhD (Main Supervisor): Ana Rita Moura Polónia (CESAM member)

PhD (Co-supervisor): Marina Ferreira (CESAM member)

PhD (Co-supervisor): Thomas Swierts (not a CESAM member)

PhD (Co-supervisor): Lisa Becking (not a CESAM member)

PhD (Co-supervisor): Diogo Pinho (ex-CESAM member)

PhD (Co-supervisor): Ana Cecília da Cruz Pires (ex-CESAM member)

PhD (Co-supervisor): Esther van der Ent (not a CESAM member)

Post-doc (Co-supervisor): Francisco José Riso da Costa Coelho (ex-CESAM member)

Reviewer for International Journals

Acta Oecologica

Biodiversity and Conservation

• Contributions to Zoology

Conservation Biology

Diversity and Distributions


Ecological Entomology


Entomological Science

Estuarine, Coastal and Shelf Science

FEMS Microbiology Ecology

Journal of Applied Ecology

Journal of Biogeography

Journal of Tropical Ecology

Journal of Tropical Forest Science

Landscape Ecology

Marine Ecology Progress Series

Molecular Ecology



Western North American Naturalist

Short history

Principal researcher of Marine and Estuarine Ecology. I studied biology at the University of Amsterdam. During my study I spent half a year in the Caribbean where I studied aggressive interactions among coral species. After this I spent a year in France at the Université de Provence. For my PhD (also in Amsterdam), I spent two and a half years in the jungles of Borneo, mainly studying butterflies but I was also interested in many other organisms in the rainforest and how disturbances such as logging and forest fires affected them. After my PhD, I did postdocs in Amsterdam and Leiden. Author of more than 100 papers in leading international journals in the areas of Ecology, Tropical Biology and Marine Biology. Principal Researcher or team member of national and international research projects on terrestrial and marine ecology. Research advisor of several Msc students, PhD students and Postdocs. Has refereed several leading journals in the fields of ecology, conservation biology, zoology and marine biology. My major interests include corals, sponges, butterflies, odonates, microbial ecology, biostatistics (particularly using R) and relating community structure to spatial, environmental and temporal processes.

CESAM Funding: UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020


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