Oliveira V., Polónia A.R.M., Cleary D.F.R., Huang Y.u.s.h.e.n.g. .M., de Voogd N.J., Keller-Costa T., Costa R., Gomes N.C.M. (2022) Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts.
Microbiological Research, 265
.
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Cleary, D.F.R., Polónia, A.R.M., Swierts, T., Coelho, F.J.R.C., de Voogd, N.J., Gomes, N.C.M. (2022) Spatial and environmental variables structure sponge symbiont communities.
Molecular Ecology, 31
, (19), 4932-4948.
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Ferreira M.R., Cleary D.F.R., Bat N.K., Polónia A.R., Gomes, N.C.M. (2022) Assessing the core microbial symbionts of jellyfish in Indonesian and Vietnamese marine lakes.
Journal Of The Marine Biological Association Of The United Kingdom,
486-494.
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Oliveira V., Polonia A.R.M., Cleary D.F.R., Huang Y.S.M., de Voogd N.J., da Rocha U.N., Gomes N.C.M. (2021) Characterization of putative circular plasmids in sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification.
MOLECULAR ECOLOGY RESOURCES, 21
, (1), 110-121.
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Cleary D.F.R., Polonia A.R.M., Huang Y.M., Swierts T. (2020) Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY,
.
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Ferreira M.R.S., Cleary D.F.R., Coelho F.J.R.C., Gomes N.C.M., Huang Y.M., Polonia A.R.M., de Voogd N.J. (2020) Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor.
ANNALS OF MICROBIOLOGY, 70
, (1), .
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Polonia A.R.M., Cleary D.F.R., Gauvin-Bialecki A., de Voogd N.J. (2020) Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY,
.
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Daniel F.R.C., Ana R.M.P. (2020) Marine lake populations of jellyfish, mussels and sponges host compositionally distinct prokaryotic communities.
HYDROBIOLOGIA, 847
, (16), 3409-3425.
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Pires, ACC, Oliveira, V, Cleary, DFR, Polónia AR, Coelho, FJRC, Waheed, Z, de Voogd, NJ, Gomes, NCM (2020) Bacterial composition and putative functions associated with sponges, sediment and seawater from the Tioman coral reef system, Peninsular Malaysia.
Marine Biology Research, 16
729-743.
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Cleary D.F.R., Ferreira M.R.S., Bat N.K., Polonia A.R.M., Gomes N.C.M., de Voogd N.J. (2020) Bacterial composition of sponges, sediment and seawater in enclosed and open marine lakes in Ha Long Bay Vietnam.
MARINE BIOLOGY RESEARCH, 16
, (1), 18-31.
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Polonia A.R.M., Cleary D.F.R., Duine A.A., Van Dijk J., De Voogd N.J. (2019) Assessment of fish community structure along the Jakarta Bay-Pulau Seribu reef complex.
JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, 99
, (2), 503-516.
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Cleary D.F.R., Swierts T., Coelho F.J.R.C., Polonia A.R.M., Huang Y.S.M., Ferreira M.R.S., Putchakarn S., Carvalheiro L., van der Ent E., Ueng J.P., Gomes N.C.M., de Voogd N.J. (2019) The sponge microbiome within the greater coral reef microbial metacommunity.
NATURE COMMUNICATIONS, 10
.
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Pires A.C.C., Cleary D.F.R., Polonia A.R.M., Lim S.C., De Voogd N.J., Oliveira V., Gomes N.C.M. (2019) Comparison of bacterial communities associated with Xestospongia testudinaria, sediment and seawater in a Singaporean coral reef ecosystem.
JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, 99
, (2), 331-342.
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Cleary D.F.R., Polonia A.R.M., Huang Y.M., Putchakarn S., Gomes N.C.M., de Voogd N.J. (2019) A comparison of prokaryote communities inhabiting sponges, bacterial mats, sediment and seawater in Southeast Asian coral reefs.
FEMS MICROBIOLOGY ECOLOGY, 95
, (12), .
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Polonia A.R.M., Cleary D.F.R. (2019) Archaeal communities in sponge, sediment and water from marine lakes and open water habitats.
MARINE BIOLOGY RESEARCH, 15
, (3), 259-274.
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Coelho F.J.R.C., Cleary D.F.R., Gomes N.C.M., Polonia A.R.M., Huang Y.M., Liu L.L., de Voogd N.J. (2018) Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems.
MICROBIAL ECOLOGY, 75
, (1), 239-254.
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Cleary D.F.R., Polonia A.R.M. (2018) Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, 111
, (2), 237-257.
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Cleary D.F.R., Polonia A.R.M., de Voogd N.J. (2018) Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes.
FEMS MICROBIOLOGY ECOLOGY, 94
, (2), .
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Cleary D.F.R., Polonia A.R.M., de Voogd N.J. (2018) Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea.
MICROBIAL ECOLOGY, 76
, (3), 610-624.
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Cleary D.F.R., Polonia A.R.M., Becking L.E., de Voogd N.J., Purwanto ., Gomes H., Gomes N.C.M. (2018) Compositional analysis of bacterial communities in seawater, sediment and high and low microbial abundance sponges in the Misool coral reef system, Indonesia.
MARINE BIODIVERSITY, 48
, (4), 1889-1901.
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de Voogd N.J., Gauvin-Bialecki A., Polonia A.R.M., Cleary D.F.R. (2018) Assessing the bacterial communities of sponges inhabiting the remote western Indian Ocean island of Mayotte.
MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE, 39
, (6), .
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Luciana Albuquerque ., Ana Rita Polónia ., Cristina Barroso ., Hugo J. C. Froufe ., Olga Lage ., Alexandre Lobo-da Cunha ., Conceição Egas ., Milton S. da Costa . (2018) Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov.
International Journal Of Systematic And Evolutionary Microbiology,
.
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Polonia A.R.M., Cleary D.F.R., Coelho F.J.R.D., Becking L.E., de Voogd N.J., Toha A.H.A., Gomes N.C.M. (2018) Compositional analysis of archaeal communities in high and low microbial abundance sponges in the Misool coral reef system, Indonesia.
MARINE BIOLOGY RESEARCH, 14
, (6), 537-550.
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Cleary D.F.R., Coelho F.J.R.C., Oliveira V., Gomes N.C.M., Polonia A.R.M. (2017) Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment.
Marine Ecology, 38
, (2), -e12411.
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Polonia A.R.M., Cleary D.F.R., Freitas R., Gomes N.C.M., de Voogd N.J. (2017) Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment.
JOURNAL OF SEA RESEARCH, 119
37-53.
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Polonia A.R.M., Cleary D.F.R., Freitas R., Coelho F.J.R.C., de Voogd N.J., Gomes N.C.M. (2016) Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment.
MARINE GENOMICS, 29
69-80.
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Cleary D.F.R., Becking L.E., Polonia A.R.M., Freitas R.M., Gomes N.C.M. (2016) Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes.
FEMS MICROBIOLOGY ECOLOGY, 92
, (5), .
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Coelho F.J.R.C., Cleary D.F.R., Costa R., Ferreira M., Polonia A.R.M., Silva A.M.S., Simoes M.M.Q., Oliveira V., Gomes N.C.M. (2016) Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.
MOLECULAR ECOLOGY, 25
, (18), 4645-4659.
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Cleary D.F.R., Polonia A.R.M., Sousa A.I., Lillebo A.I., Queiroga H., Gomes N.C.M. (2016) Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.
PLANT BIOLOGY, 18
, (5), 824-834.
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Cleary D.F.R., Polonia A.R.M., Renema W., Hoeksema B.W., Rachello-Dolmen P.G., Moolenbeek R.G., Budiyanto A., Yahmantoro ., Tuti Y., Giyanto ., Draisma S.G.A., van Reine W.F.P., Hariyanto R., Gittenberger A., Rikoh M.S., de Voogd N.J. (2016) Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.
MARINE POLLUTION BULLETIN, 110
, (2), 701-717.
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Cleary D.F.R., Becking L.E., Polonia A.R.M., Freitas R.M., Gomes N.C.M. (2015) Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, 107
, (3), 821-834.
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de Voogd N.J., Cleary D.F.R., Polonia A.R.M., Gomes N.C.M. (2015) Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia.
FEMS MICROBIOLOGY ECOLOGY, 91
, (4), .
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Pegoraro N., Calado R., Duarte L.N., Manco S.C., Fernandes F.J., Polonia A.R.M., Cleary D.E.R., Gomes N.C.M. (2015) Molecular analysis of skin bacterial assemblages from codfish and pollock after dry-salted fish production.
JOURNAL OF FOOD PROTECTION, 78
, (5), 983-989.
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Polonia A.R.M., Cleary D.F.R., Freitas R., de Voogd N.J., Gomes N.C.M. (2015) The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment.
MOLECULAR ECOLOGY, 24
, (2), 409-423.
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Cleary D.F.R., de Voogd N.J., Polonia A.R.M., Freitas R., Gomes N.C.M. (2015) Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia.
MICROBIAL ECOLOGY, 70
, (4), 889-903.
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Polonia A.R.M., Cleary D.F.R., de Voogd N.J., Renema W., Hoeksema B.W., Martins A., Gomes N.C.M. (2015) Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago.
SCIENCE OF THE TOTAL ENVIRONMENT, 537
139-151.
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Polonia A.R.M., Cleary D.F.R., Duarte L.N., de Voogd N.J., Gomes N.C.M. (2014) Composition of Archaea in Seawater, Sediment, and Sponges in the Kepulauan Seribu Reef System, Indonesia.
Microbial Ecology, 67
, (3), 553-567. 1432-184X.
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Cleary D.F.R., Polonia A.R.M., Renema W., Hoeksema B.W., Wolstenholme J., Tuti Y., de Voogd N.J. (2014) Coral reefs next to a major conurbation: a study of temporal change (1985-2011) in coral cover and composition in the reefs of Jakarta, Indonesia.
Marine Ecology Progress Series, 501
89-98.
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Cleary D.F.R., Becking L.E., de Voogd N.J., Pires A.C.C., Polónia A.R.M., Egas C., Gomes N.C.M. (2013) Habitat and host related variation in sponge bacterial symbiont communities in Indonesian waters.
FEMS Microbiology Ecology, 85
, (3), 465–482.
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Polonia A.R., Figueiredo M., Cleary D.F.R., de Voogd N.J., Martins A. (2011) Sea surface temperature and ocean colour (MODIS/AQUA) space and time variability in Indonesian Sea coral reef systems from 2002 to 2011.
REMOTE SENSING OF THE OCEAN, SEA ICE, COASTAL WATERS, AND LARGE WATER REGIONS 2011, 8175
. 978-0-81948-802-2.
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Oliveira V., Polónia A.R.M, Cleary D.F.R., Yusheng M.A., de Voogd N.J., Rocha U.N., Gomes N.C.M. (2019) Amplification of Plasmid DNA from sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification. 15th Symposium on Bacterial Genetics and Ecology, 26–30 May 2019, Lisbon, Portugal.
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Polónia, A. R. M., Vanessa Oliveira, Rodolfo B. Toscan, João P. Saraiva, Ulisses N. da Rocha, Nicole J. de Voogd, Yusheng M. Huang, Daniel F.R. Cleary, Newton C.M. Gomes (2019) Metagenomic analysis of the sponge Cinachyrella sp., seawater and sediment of a Taiwanese coral reef ecosystem. Microbiotec’19, 5 to 7 December, 2019, Coimbra.
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Vanessa Oliveira, Polónia, A. R. M., Daniel R.F. Cleary, Yusheng M. Huang, Nicole J. de Voogd, Ulisses N. da Rocha, Newton C.M. Gomes (2019) Plasmid diversity of bacterial communities associated with the marine sponge Cinachyrella sp. Microbiotec’19 , 5 to 7 December, 2019, Coimbra.
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Oliveira V., Pires A.C.C., Cleary D.F.R., Pólonia A.R.M., Lim S.C., de Voogd N.J., Gomes N.C.M. (2017) Bacterial communities of Xestospongia testudinaria, sediment and water in a singaporean coral reef ecosystem. BAGECO 2017- 14th Symposium on Bacterial Genetics and Ecology., June 4-8, Aberdeen, Scotland.
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Sousa A.I., Polónia A.R., Calado R., Serôdio J., Cleary D.F.R., Lillebø A.I. (2014) Zostera noltii functioning and dynamics along a salinity gradient: Ria de Aveiro (Portugal). Seagrasses in Europe: Threats, Responses and Management, 4-6 March, 2014, Olhão, Faro, Portugal.
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Sousa A.I., Polónia A.R., Calado R., Serôdio J., Cleary D.F.R., Lillebø A.I. (2013) Zostera noltii dynamics along a salinity gradient: Ria de Aveiro (Portugal). 8th International SedNet conference, 6-9 November, Lisbon, Portugal.
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Polónia ARM, Cleary DRF, Duarte LN, de Voogd NJ, Gomes NCM Composition of Archaea in seawater, sediment and sponges in the Kepulauan Seribu reef system, Indonesia. First EMBO Conference on Aquatic Microbial Ecology: SAME13, , Stresa, Italy.
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Polónia ARM, Figueiredo M, Cleary DFR, de Voogd NJ, Martins A. Sea surface temperature and ocean colour (MODIS/AQUA) space and time variability in Indonesian Sea coral reef systems from 2002 to 2011. Remote Sensing of the Ocean, Sea Ice, Coastal Waters, and Large Water Regions 2011 , , Prague, Czech Republic.
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ARM Polónia, DFR Cleary, LN Duarte, NJ de Voogd, NCM Gomes Composition and diversity of Archaea in seawater, sediment and sponges in the Kepulauan Seribu reef system, Java, Indonesia. Ninth World Sponge Conference 2013, , Fremantle, Western Australia.
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Nicole de Voogd, Daniel FR Cleary, Ana RM Polónia, Newton CM Gomes Community structure of Archaea and Bacteria in two Indonesian sponges. Ninth World Sponge Conference 2013, Fremantle, Western Australia, .
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Rossana M. Freitas, Daniel F.R. Cleary, Ana R.M. Polónia, Leontine E. Becking, Newton C.M. Gomes Diversity of bacterial community in mussels from Indonesian marine lakes. First EMBO Conference on Aquatic Microbial Ecology: SAME13, , Stresa, Italy.
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Nicole J de Voogd, Daniel FR Cleary, Ana RM Polónia, Anne Bialecki, Newton CM Gomes The Microbial Communities Inhabiting Sponges of the Remote Western Indian Ocean Island of Mayotte. 2nd International Symposium on Sponge Microbiology, October 26-29, 2014, Baltimore, Maryland, USA.
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