Hostname: page-component-586b7cd67f-l7hp2 Total loading time: 0 Render date: 2024-11-23T12:06:36.291Z Has data issue: false hasContentIssue false
  • English
  • Français

Periphyton diversity in two different Antarctic lakes assessed using metabarcoding

Published online by Cambridge University Press:  20 September 2021

Paulo E.A.S. Câmara Open the ORCID record for Paulo E.A.S. Câmara [Opens in a new window] ,
Láuren M.D. De Souza Open the ORCID record for Láuren M.D. De Souza [Opens in a new window] ,
Otávio Henrique Bezerra Pinto Open the ORCID record for Otávio Henrique Bezerra Pinto [Opens in a new window] ,
Peter Convey Open the ORCID record for Peter Convey [Opens in a new window] ,
Eduardo T. Amorim Open the ORCID record for Eduardo T. Amorim [Opens in a new window] ,
Micheline Carvalho-Silva Open the ORCID record for Micheline Carvalho-Silva [Opens in a new window]  and
Luiz Henrique Rosa Open the ORCID record for Luiz Henrique Rosa [Opens in a new window]
Paulo E.A.S. Câmara*
Affiliation:
Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, Brazil
Láuren M.D. De Souza
Affiliation:
Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901, Brazil
Otávio Henrique Bezerra Pinto
Affiliation:
Departamento deBiologia Celular, Universidade de Brasília, Brasília, 70910-900, Brazil
Peter Convey
Affiliation:
British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK
Eduardo T. Amorim
Affiliation:
Centro Nacional de Conservação da Flora/Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (CNCFlora/JBRJ), Rio de Janeiro, 22.460-030, Brazil
Micheline Carvalho-Silva
Affiliation:
Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, Brazil
Luiz Henrique Rosa
Affiliation:
Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901, Brazil
*
pcamara@unb.br
Get access Rights & Permissions [Opens in a new window]

Abstract

Antarctic lakes have generally simple periphyton communities when compared with those of lower latitudes. To date, assessment of microbial diversity in Antarctica has relied heavily on traditional direct observation and cultivation methods. In this study, sterilized cotton baits were left submerged for two years in two lakes on King George Island and Deception Island, South Shetland Islands (Maritime Antarctic), followed by assessment of diversity by metabarcoding using high-throughput sequencing. DNA sequences of 44 taxa belonging to four kingdoms and seven phyla were found. Thirty-six taxa were detected in Hennequin Lake on King George Island and 20 taxa were detected in Soto Lake on Deception Island. However, no significant difference in species composition was detected between the two assemblages (Shannon index). Our data suggest that metabarcoding provides a suitable method for the assessment of periphyton biodiversity in oligotrophic Antarctic lakes.

Keywords

Deception Islandhigh-throughput sequencinginternal transcribed spacerKing George Island
Type
Biological Sciences
Information
Antarctic Science , Volume 33 , Issue 6 , December 2021 , pp. 596 - 604
Check for updates
Copyright
Copyright © Antarctic Science Ltd 2021

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abarenkov, K., Zirk, A., Piirmann, T., Pöhönen, R., Ivanov, F., Nilsson, R.H. & Kõljalg, U. 2020. UNITE QIIME release for Fungi [data set]. Version 04.02.2020. UNITE Community, 10.15156/BIO/786385.Google Scholar
Banchi, E., Ametrano, C.G., Greco, S., Stanković, D., Muggia, L. & Pallavicini, A. 2020. PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding. Database, 2020, 10.1093/database/baz155.CrossRefGoogle ScholarPubMed
Bardou, P., Mariette, J., Escudié, F., Djemiel, C. & Klopp, C. 2014. Jvenn: an interactive Venn diagram viewer. BMC Bioinformatics, 15, 10.1186/1471-2105-15-293.CrossRefGoogle ScholarPubMed
Bokulich, N.A., Kaehler, B.D., Rideout, J.R., Dillon, M., Boylern, E., Knight, R., et al. 2018. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome, 6, 10.1186/s40168-018-0470-z.CrossRefGoogle ScholarPubMed
Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., et al. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 10, 10.1038/nmeth.2276.CrossRefGoogle ScholarPubMed
Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-ghalith, A., Alexander, H., et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 10.1038/s41587-019-0209-9.Google ScholarPubMed
Buck, K.R. & Garrison, D.L. 1988. Distribution and abundance of choanoflagellates (Acanthoecidae) across the ice-edge zone in the Weddell Sea, Antarctica. Marine Biology, 98, 10.1007/BF00391204.CrossRefGoogle Scholar
Butler, H.G., Edworthy, M.G. & Ellis-Evans, J.C. 2000. Temporal plankton dynamics in an oligotrophic Maritime Antarctic lake. Freshwater Biology, 43, 10.1046/j.1365-2427.2000.00542.x.CrossRefGoogle Scholar
Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A. & Holmes, S.P. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 10.1038/nmeth.3869.CrossRefGoogle ScholarPubMed
Câmara, P.E.A.S., Carvalho-Silva, M., Pinto, O.H.B., Amorim, E.T., Henriques, D.K., Silva, T.H., et al. 2020. Diversity and ecology of Chlorophyta (Viridiplantae) assemblages in protected and non-protected sites in Deception Island (Antarctica, South Shetland Islands) assessed using an NGS approach. Microbial Ecology, 81, 10.1007/s00248-020-01584-9.Google ScholarPubMed
Cavalier-Smith, T. 2007. A revised six-kingdom system of life. Biological Reviews, 73, 10.1111/j.1469-185X.1998.tb00030.x.CrossRefGoogle Scholar
Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., et al. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One, 5, 10.1371/journal.pone.0008613.Google ScholarPubMed
Convey, P., Chown, S.L., Clarke, A., Barnes, D.K.A., Bokhorst, S., Cummings, V., et al. 2014. The spatial structure of Antarctic biodiversity. Ecological Monographs, 84, 10.1890/12-2216.1.CrossRefGoogle Scholar
de Souza, L.M.D., Ogaki, M.B., Câmara, P.E.A.S., Pinto, O.H.B., Convey, P., Carvalho-Silva, M., et al. 2021. Assessment of fungal diversity present in lakes of Maritime Antarctica using DNA metabarcoding: a temporal microcosm experiment. Extremophiles, 25, 10.1007/s00792-020-01212-x.CrossRefGoogle ScholarPubMed
Deiner, K., Bik, H.M., Mächler, E., Seymour, M., Lacoursière-Roussel, A., Altermatt, F., et al. 2017. Environmental DNA metabarcoding: transforming how we survey animal and plant communities. Molecular Ecology, 26, 10.1111/mec.14350.CrossRefGoogle ScholarPubMed
Fraser, C.I., Connell, L., Lee, C.K. & Cary, S.C. 2018. Evidence of plant and animal communities at exposed and subglacial (cave) geothermal sites in Antarctica. Polar Biology, 41, 10.1007/s00300-017-2198-9.CrossRefGoogle Scholar
Garrido-Benavent, I., Pérez-Ortega, S., Durán, J., Ascaso, C., Pointing, S.B., Rodríguez-Cielos, R., et al. 2020. Differential colonization and succession of microbial communities in rock and soil substrates on a Maritime Antarctic glacier forefield. Frontiers in Microbiology, 11, 10.3389/fmicb.2020.00126.CrossRefGoogle ScholarPubMed
Giner, C.R., Forn, I., Romac, S., Logares, R.C. & Massana, R. 2016. Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes. Applied and Environmental Microbiology, 82, 10.1128/AEM.00560-16.CrossRefGoogle ScholarPubMed
Gonçalves, V.N., Vaz, A.B.N., Rosa, C.A. & Rosa, L.H. 2012. Diversity and distribution of fungal communities in lakes of Antarctica. FEMS Microbiology Ecology, 82, 10.1111/j.1574-6941.2012.01424.x.CrossRefGoogle ScholarPubMed
Greenslade, P. 1995. Collembola from the Scotia Arc and Antarctic Peninsula including descriptions of two new species and notes on biogeography. Polskie Pismo Entomologiczne, 64, 305–319.Google Scholar
Greenslade, P., Potapov, M., Russel, R. & Convey, P. 2012. Global Collembola on Deception Island. Journal of Insect Science, 12, 10.1673/031.012.11101.CrossRefGoogle ScholarPubMed
Hammer, Ø., Harper, D.A.T. & Ryan, P.D. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 1–9.Google Scholar
Hansson, L-A. 1992. Factors regulating periphytic algal biomass. Limnology and Oceanography, 37, 10.4319/lo.1992.37.2.0322.CrossRefGoogle Scholar
Hansson, L.A., Hylander, S., Dartnall, H.J., Lidstrom, S. & Svensson, J.E. 2012. High zooplankton diversity in the extreme environments of the McMurdo Dry Valley lakes, Antarctica. Antarctic Science, 24, 10.1017/S095410201100071X.CrossRefGoogle Scholar
Hering, D., Borja, A., Jones, J.I., Pont, D., Boets, P., Bouchez, A., et al. 2018. Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research, 138, 10.1016/j.watres.2018.03.003.CrossRefGoogle ScholarPubMed
Huss, V., Frank, C., Hartmann, E.C. & Hirmer, M. 1999. Biochemical taxonomy and molecular phylogeny of the genus Chlorella sensu lato (Chlorophyta). Journal of Phycology, 35, 10.1046/j.1529-8817.1999.3530587.x.CrossRefGoogle Scholar
Izaguirre, I., Allende, L. & Schiaffino, M.R. 2020. Phytoplankton in Antarctic lakes: biodiversity and main ecological features. Hydrobiologia, 848, 10.1007/s10750-020-04306-x.Google Scholar
Izaguirre, I., Allende, L. & Tell, G. 2006. Algal communities of a geothermally heated lagoon on Deception Island (South Shetland Islands). Polar Biology, 29, 10.1007/s00300-005-0065-6.CrossRefGoogle Scholar
Jungblut, A.-D., Hawes, I., Mountfort, D., Hitzfeld, B., Dietrich, D.R., Burns, B.P. & Neilan, B.A. 2005. Diversity within cyanobacterial mat communities in variable salinity meltwater ponds of McMurdo Ice Shelf, Antarctica. Environmental Microbiology, 7, 10.1111/j.1462-2920.2005.00717.x.CrossRefGoogle ScholarPubMed
Laybourn-Parry, J. & Pearce, D.A. 2007. The biodiversity and ecology of Antarctic lakes: models for evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 362, 10.1098/rstb.2006.1945.CrossRefGoogle ScholarPubMed
Leadbeater, B.S. & Kelly, M. 2001. Evolution of animals - choanoflagellates and sponges. Water and Atmosphere Online, 9, 9–11.Google Scholar
Leliaert, F., Smith, D.R., Moreau, H., Herron, M.D., Verbruggen, H., Delwiche, C.F. & De Clerck, O. 2012. Phylogeny and molecular evolution of the green algae. Critical Reviews in Plant Science, 31, 10.1080/07352689.2011.615705.CrossRefGoogle Scholar
Mataloni, G. & Pose, M. 2001. Non-marine algae from islands near Cierva Point, Antarctic Peninsula. Cryptogamie Algologie, 22, 10.1016/S0181-1568(00)01049-7.CrossRefGoogle Scholar
Medinger, R., Nolte, V., Pandey, R.V., Jost, S., Ottenwalder, B., Schlotterer, C. & Boenigk, J. 2010. Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology, 19, 10.1111/j.1365-294X.2009.04478.x.CrossRefGoogle Scholar
Ogaki, M.B., Vieira, R., Lírio, J.M., Rosa, C.A. & Rosa, L.H. 2019. Diversity and ecology of fungal assemblages present in lakes of Antarctica. In Rosa, L.H., ed. Fungi of Antarctica. Cham: Springer Nature, 69–97.CrossRefGoogle ScholarPubMed
Ogaki, M.B., Pinto, O.H.B., Vieira, R., Neto, A.A., Convey, P., Carvalho-Silva, M., et al. 2021. Fungi present in Antarctic deep-sea sediments assessed using DNA metabarcoding. Microbial Ecology, 10.1007/s00248-020-01658-8.CrossRefGoogle ScholarPubMed
Ogaki, M.B., Vieira, R., Muniz, M.C., Zani, C.L., Alves, T.M.A., Junior, P.A.S., et al. 2020. Diversity, ecology, and bioprospecting of culturable fungi in lakes impacted by anthropogenic activities in Maritime Antarctica. Extremophiles, 24, 10.1007/s00792-020-01183-z.CrossRefGoogle ScholarPubMed
Park, J.S. & Simpson, A.G.B. 2011. Characterization of Pharyngomonas kirbyi (='Macropharyngomonas halophila' nomen nudum), a very deep-branching, obligately halophilic heterolobosean flagellate. Protist, 162, 10.1016/j.protis.2011.05.004.CrossRefGoogle Scholar
Peters, J.A. & Lodge, D.M. 2009. Littoral zone. In Likens, G.E., ed. Encyclopedia of inland waters. Cambridge, MA: Academic Press, 79–87.CrossRefGoogle Scholar
Richardson, R.T., Lin, C., Sponsler, D.B., Quijia, J.O., Goodell, K. & Johnson, R. M. 2015. Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem. Applications in Plant Sciences, 3, 10.3732/apps.1400066.CrossRefGoogle Scholar
Rippin, M., Borchhardt, N., Williams, L., Colesie, C., Jung, P., Büdel, B., et al. 2018. Genus richness of microalgae and cyanobacteria in biological soil crusts from Svalbard and Livingston Island: morphological versus molecular approaches. Polar Biology, 41, 10.1007/s00300-018-2252-2.CrossRefGoogle Scholar
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ, 4, 10.7717/peerj.2584.CrossRefGoogle ScholarPubMed
Rosa, L.H., Da Silva, T.H., Ogaki, M.B., Pinto, O.H.B., Stech, M., Convey, P., et al. 2020. DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica. Scientific Reports, 10, 10.1038/s41598-020-78934-7.CrossRefGoogle ScholarPubMed
Ruppert, K., Kline, R.J. & Rahman, M. S. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation, 17, 10.1016/j.gecco.2019.e00547.CrossRefGoogle Scholar
Weber, A.A. & Pawlowski, J. 2013. Can abundance of protists be inferred from sequence data: a case study of Foraminifera. PLoS One, 8, 10.1371/journal.pone.0056739.CrossRefGoogle ScholarPubMed
White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J., eds. PCR protocols: a guide to methods and applications. Cambridge, MA: Academic Press, 315–322.Google Scholar
Wood, S.A., Kuhajek, J.M., De Winton, M. & Phillips, N.R. 2012. Species composition and cyanotoxin production in periphyton mats from three lakes of varying trophic status. FEMS Microbiology Ecology, 79, 10.1111/j.1574-6941.2011.01217.x.CrossRefGoogle ScholarPubMed