Sea-level rise in northern Australia’s Kakadu National Park: a survey of floodplain eukaryotes
Sarah A. Stephenson A E , Tiffanie M. Nelson B , Claire Streten B , Karen S. Gibb C , David Williams B , Paul Greenfield A D and Anthony A. Chariton A D
+ Author Affiliations
- Author Affiliations
A CSIRO Oceans and Atmosphere, Locked Bag 2007, Kirrawee, NSW 2232, Australia.
B Australian Institute of Marine Science, Sustainable Coastal Ecosystems and Industries in Tropical Australia, Arafura Timor Research Facility, 23 Ellengowan Drive, Casuarina, NT 0810, Australia.
C Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0810, Australia.
D Environmental Genomics, Ecology and Ecotoxicology Lab (EGEEL), Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
E Corresponding author. Email: sarah.stephenson@csiro.au
Marine and Freshwater Research 69(7) 1134-1145 https://doi.org/10.1071/MF18067
Submitted: 26 February 2018 Accepted: 29 April 2018 Published: 12 June 2018
Abstract
Forecasted climate-change models predict that much of northern Australia’s coastal habitats will be in retreat because of saltwater intrusion (SWI) from sea-level rise. A region of primary concern is the nutrient-rich and biodiverse floodplains of world heritage-listed Kakadu National Park (KNP). To understand the implications of SWI, we need fundamental baseline information for floodplain biota from the South Alligator River, KNP, northern Australia, and informative data on how increased and prolonged exposure to salt is likely to shape the eukaryotic community. To assist in addressing these key knowledge gaps, we used amplicon sequencing to examine the composition of eukaryotic soil communities from the South Alligator River floodplain, an ecologically important area at the ‘coalface’ of sea-level rise. Samples were obtained from three river zones and three floodplain morphologies, capturing a wide range of habitats and episodic exposures to both saltwater and freshwater. We found that both the floodplain morphology and positioning along the river significantly influenced eukaryotic composition. However, the influence of these variables varied greatly among the floodplain morphologies, with correlative evidence suggesting that both salinity and pH played a dominant role in shaping communities within lower parts of the floodplain, with this being particularly evident in those regions subjected to major tidal influence (estuarine funnel and sinuous, and cuspate).
Additional keywords: climate change, flood morphology, metabarcoding, river zone, saltwater.
References
Baldwin, D. S., Colloff, M. J., Rees, G. N., Chariton, A. A., Watson, G. O., Court, L. N., Hartley, D. M., Morgan, M. J., King, A. J., Wilson, J. S., Hodda, M., and Hardy, C. M. (2013). Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils. Molecular Ecology 22, 1746–1758.| Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils.Crossref | GoogleScholarGoogle Scholar |
Battarbee, R. W., Charles, D. F., Bigler, C., Cumming, B. F., and Renberg, I. (2010). Diatoms as indicators of surface-water acidity. In ‘The Diatoms: Applications for the Environmental and Earth Sciences’. (Eds E. F. Stoermer and J. P. Smol.) pp. 98–121. (Cambridge University Press: Cambridge, UK.)
Bayliss, P., and Ligtermoet, E. (2018). Seasonal habitats, decadal trends in abundance and cultural values of magpie geese (Anseranus semipalmata) on coastal floodplains in the Kakadu Region, northern Australia. Marine and Freshwater Research 69, 1079–1091.
| Seasonal habitats, decadal trends in abundance and cultural values of magpie geese (Anseranus semipalmata) on coastal floodplains in the Kakadu Region, northern Australia.Crossref | GoogleScholarGoogle Scholar |
Bayliss, P., Saunders, K., Dutra, L. X. C., Melo, L. F. C., Hilton, J., Prakash, M., and Woolard, F. (2018a). Assessing sea level-rise risks to coastal floodplains in the Kakadu Region, northern Australia, using a tidally driven hydrodynamic model. Marine and Freshwater Research 69, 1064–1078.
| Assessing sea level-rise risks to coastal floodplains in the Kakadu Region, northern Australia, using a tidally driven hydrodynamic model.Crossref | GoogleScholarGoogle Scholar |
Bayliss, P., Finlayson, C. M., Innes, J. A., Norman-López, A., Bartolo, R., Harford, A., Pettit, N. E., Humphrey, C. L., van Dam, R., Dutra, L. X. C., Woodward, E., Ligtermoet, E., Steven, A., Chariton, A., and Williams, D. K. (2018b). An integrated risk-assessment framework for multiple threats to floodplain values in the Kakadu Region, Australia, under a changing climate. Marine and Freshwater Research 69, 1159–1185.
| An integrated risk-assessment framework for multiple threats to floodplain values in the Kakadu Region, Australia, under a changing climate.Crossref | GoogleScholarGoogle Scholar |
Bohmann, K., Evans, A., Thomas, M., Gilbert, P., Carvalho, G. R., Creer, S., Knapp, M., Yu, D. W., and de Bruyn, M. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution 29, 358–367.
| Environmental DNA for wildlife biology and biodiversity monitoring.Crossref | GoogleScholarGoogle Scholar |
Brady, N. C., and Weil, R. R. (2009). ‘Organisms and Ecology of the Soil. Elements of the Nature and Properties of Soils’, 3rd edn. (Prentice Hall: Upper Saddle River, NJ, USA.)
Brock, M. A., Nielsen, D. L., and Crosslé, K. (2005). Changes in biotic communities developing from freshwater wetland sediments under experimental salinity and water regimes. Freshwater Biology 50, 1376–1390.
| Changes in biotic communities developing from freshwater wetland sediments under experimental salinity and water regimes.Crossref | GoogleScholarGoogle Scholar |
Bücking, H., Liepold, E., and Ambilwade, P. (2012). The role of the Mycorrhizal symbiosis in nutrient uptake of plants and the regulatory mechanisms underlying these transport processes. In ‘Plant Science’. (Ed. N. K. Dhal.) Chapter 4, pp. 120–121. (IntechOpen: London, UK.)
Chariton, A. A., Stephenson, S., Morgan, M. J., Steven, A. D. L., Colloff, M. J., Court, L. N., and Hardy, C. M. (2015). Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries. Environmental Pollution 203, 165–174.
| Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries.Crossref | GoogleScholarGoogle Scholar |
Cobb, S. M. (1997). Channel extension and the geomorphology of tidal creeks in Kakadu national park, Northern Territory. B.Sc.(Hons) Thesis, University of Western Australia, Perth, WA, Australia.
Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras-Alfaro, A., Kuske, C. R., and Tiedje, J. M. (2014). Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42, D633–D642.
| Ribosomal Database Project: data and tools for high throughput rRNA analysis.Crossref | GoogleScholarGoogle Scholar |
Davis, J. A., McGuire, M., Halse, S. A., Hamilton, D., Horwitz, P., McComb, A. J., Froend, R. H., Lyons, M., and Sim, L. (2003). What happens when you add salt: predicting impacts of secondary salinisation on shallow aquatic ecosystems by using an alternative-states model. Australian Journal of Botany 51, 715–724.
| What happens when you add salt: predicting impacts of secondary salinisation on shallow aquatic ecosystems by using an alternative-states model.Crossref | GoogleScholarGoogle Scholar |
De Cáceres, M., and Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology 90, 3566–3574.
| Associations between species and groups of sites: indices and statistical inference.Crossref | GoogleScholarGoogle Scholar |
Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10, 996–998.
| UPARSE: highly accurate OTU sequences from microbial amplicon reads.Crossref | GoogleScholarGoogle Scholar |
Egge, E., Bittner, L., Andersen, T., Audic, S., de Vargas, C., and Edvardsen, B. (2013). Pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One 8, e74371.
| Pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.Crossref | GoogleScholarGoogle Scholar |
Findlay, S. E., and Kelly, V. R. (2011). Emerging indirect and long-term road salt effects on ecosystems. Annals of the New York Academy of Sciences 1223, 58–68.
| Emerging indirect and long-term road salt effects on ecosystems.Crossref | GoogleScholarGoogle Scholar |
Finlayson, C. M., Davis, J. A., Gell, P. A., Kingsford, R. T., and Parton, K. A. (2013). The status of wetlands and the predicted effects of global climate change: the situation in Australia. Aquatic Sciences 75, 73–93.
| The status of wetlands and the predicted effects of global climate change: the situation in Australia.Crossref | GoogleScholarGoogle Scholar |
Fritz, S. C., Cumming, B. F., Gasse, F., and Laird, K. R. (2010). Diatoms as indicators of hydrologic and climatic change in saline lakes. In ‘The Diatoms: Applications for the Environmental and Earth Sciences’. E. (Eds F. Stoermer and J. P. Smol.) pp. 186–208. (Cambridge University Press: Cambridge. UK)
Gardham, S., Hose, G. C., Stephenson, S., and Chariton, A. A. (2014). Chapter three: DNA metabarcoding meets experimental ecotoxicology: advancing knowledge on the ecological effects of copper in freshwater ecosystems. In ‘Advances in Ecological Research. Vol. 51’. (Eds G. Woodward, D. J. Baird., and M. Hajibabaei.) pp. 79–104. (Academic Press. Cambridge, MA, USA)
Hammer, U. T. (1986). ‘Saline Lake Ecosystems of the World.’ (Junk: Dordrecht, Netherlands.)
Hardy, C. M., Krull, E. S., Hartley, D. M., and Oliver, R. L. (2010). Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool. Molecular Ecology 19, 197–212.
| Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool.Crossref | GoogleScholarGoogle Scholar |
Hart, B. T., Bailey, P., Edwards, R., Hortle, K., James, K., McMahon, A., Meredith, C., and Swadling, K. (1991). A review of the salt sensitivity of the Australian fresh-water biota. Hydrobiologia 210, 105–144.
| A review of the salt sensitivity of the Australian fresh-water biota.Crossref | GoogleScholarGoogle Scholar |
Herbert, E. R., Boon, P., Burgin, A. J., Neubauer, S. C., Franklin, R. B., Ardón, M., Hopfensperger, K. N., Lamers, L. P. M., and Gell, P. (2015). A global perspective on wetland salinization: ecological consequences of a growing threat to freshwater wetlands. Ecosphere 6, art206.
| A global perspective on wetland salinization: ecological consequences of a growing threat to freshwater wetlands.Crossref | GoogleScholarGoogle Scholar |
Hopfensperger, K. N., Burgin, A. J., Schoepfer, V. A., and Helton, A. M. (2014). Impacts of saltwater incursion on plant communities, anaerobic microbial metabolism, and resulting relationships in a restored freshwater wetland. Ecosystems 17, 792–807.
| Impacts of saltwater incursion on plant communities, anaerobic microbial metabolism, and resulting relationships in a restored freshwater wetland.Crossref | GoogleScholarGoogle Scholar |
Isacch, J. P., Costa, C. S., Rodríguez-Gallego, B. L., Conde, D., Escapa, M., Gagliardini, D. A., and Iribarne, O. O. (2006). Distribution of saltmarsh plant communities associated with environmental factors along a latitudinal gradient on the south-west Atlantic coast. Journal of Biogeography 33, 888–900.
| Distribution of saltmarsh plant communities associated with environmental factors along a latitudinal gradient on the south-west Atlantic coast.Crossref | GoogleScholarGoogle Scholar |
James, K. R., Cant, B., and Ryan, T. (2003). Responses of freshwater biota to rising salinity levels and implications for saline water management: a review. Australian Journal of Botany 51, 703–713.
| Responses of freshwater biota to rising salinity levels and implications for saline water management: a review.Crossref | GoogleScholarGoogle Scholar |
King, R. S., and Baker, M. E. (2010). Considerations for analysing ecological community thresholds in response to anthropogenic environmental gradients. Journal of the North American Benthological Society 29, 998–1008.
| Considerations for analysing ecological community thresholds in response to anthropogenic environmental gradients.Crossref | GoogleScholarGoogle Scholar |
Kirwan, M. L., Guntenspergen, G. R., D’Alpaos, A., Morris, J. T., Mudd, S. M., and Temmerman, S. (2010). Limits on the adaptability of coastal marshes to rising sea level. Geophysical Research Letters 37, L23401.
| Limits on the adaptability of coastal marshes to rising sea level.Crossref | GoogleScholarGoogle Scholar |
Kozlowski, T. (1997). Responses of woody plants to flooding and salinity. Tree Physiology Monograph 1, 1–29.
Legendre, P., and Anderson, M. J. (1999). Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecological Monographs 69, 1–24.
| Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments.Crossref | GoogleScholarGoogle Scholar |
Lin, N., Emanuel, K., Oppenheimer, M., and Vanmarcke, E. (2012). Physically based assessment of hurricane surge threat under climate change. Nature Climate Change 2, 462–467.
| Physically based assessment of hurricane surge threat under climate change.Crossref | GoogleScholarGoogle Scholar |
Lorenz, J. J. (2014). A review of the effects of altered hydrology and salinity on vertebrate fauna and their habitats in northeastern Florida Bay. Wetlands 34, 189–200.
| A review of the effects of altered hydrology and salinity on vertebrate fauna and their habitats in northeastern Florida Bay.Crossref | GoogleScholarGoogle Scholar |
Lukacs, G. P., and Finlayson, C. M. (2010). An evaluation of ecological information on Australia’s northern tropical rivers and wetlands. Wetlands Ecology and Management 18, 597–625.
| An evaluation of ecological information on Australia’s northern tropical rivers and wetlands.Crossref | GoogleScholarGoogle Scholar |
McDonald, D., Clemente, J. C., Kuczynski, J., Rideout, J. R., Stombaugh, J., Wendel, D., Wilke, A., Huse, S., Hufnagle, J., Meyer, F., Knight, R., and Caporaso, J. G. (2012). The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1, 7.
| The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.Crossref | GoogleScholarGoogle Scholar |
Medinger, R., Nolte, V., Pandey, R. V., Jost, S., Ottenwälder, B., Schlötterer, C., and Boenigk, J. (2010). Diversity in a hidden world: potential and limitation of nextgeneration sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology 19, 32–40.
| Diversity in a hidden world: potential and limitation of nextgeneration sequencing for surveys of molecular diversity of eukaryotic microorganisms.Crossref | GoogleScholarGoogle Scholar |
Mitsch, W., and Gosselink, J. (2015). ‘Wetlands’, 5th edn. (Wiley: New York, NY, USA.)
Nelson, T. M., Streten, C., Gibb, K. S., and Chariton, A. A. (2018). Bacteria in tropical floodplain soils are sensitive to changes in saltwater. Marine and Freshwater Research 69, 1110–1123.
| Bacteria in tropical floodplain soils are sensitive to changes in saltwater.Crossref | GoogleScholarGoogle Scholar |
Neubauer, S. C., Franklin, R. B., and Berrier, D. J. (2013). Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon. Biogeosciences 10, 8171–8183.
| Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon.Crossref | GoogleScholarGoogle Scholar |
Nicholls, R. J., and Cazenave, A. (2010). Sea-level rise and its impact on coastal zones. Science 328, 1517–1520.
| Sea-level rise and its impact on coastal zones.Crossref | GoogleScholarGoogle Scholar |
Nicholls, R. J., Hoozemans, F., and Marchand, M. (1999). Increasing flood risk and wetland losses due to global sea-level rise: regional and global analyses. Global Environmental Change 9, 69–87.
| Increasing flood risk and wetland losses due to global sea-level rise: regional and global analyses.Crossref | GoogleScholarGoogle Scholar |
Nicholls, R. J., Marinova, N., Lowe, J. A., Brown, S., Vellinga, P., de Gusmao, D., Hinkel, J., and Tol, R. S. J. (2011). Sea-level rise and its possible impacts given a ‘beyond 4 degree world’ in the 21st century. Philosophical Transactions of the Royal Society of London – A. Mathematical, Physical and Engineering Sciences 369, 161–181.
| Sea-level rise and its possible impacts given a ‘beyond 4 degree world’ in the 21st century.Crossref | GoogleScholarGoogle Scholar |
Nielsen, D. L., and Brock, M. A. (2009). Modified water regime and salinity as a consequence of climate change: prospects for wetlands of southern Australia. Climatic Change 95, 523–533.
| Modified water regime and salinity as a consequence of climate change: prospects for wetlands of southern Australia.Crossref | GoogleScholarGoogle Scholar |
Nilsson, J. R., and Weidner, E. (1986). Symposium: endocytosis by and of protozoa. Insect Science and Its Application 7, 401–406.
Pettit, N. E., Bayliss, P., and Bartolo, R. (2018). Dynamics of plant communities and the impact of saltwater intrusion on the floodplains of Kakadu National Park. Marine and Freshwater Research 69, 1124–1133.
| Dynamics of plant communities and the impact of saltwater intrusion on the floodplains of Kakadu National Park.Crossref | GoogleScholarGoogle Scholar |
Pinder, A. M., Halse, S. A., McRae, J. M., and Shiel, R. J. (2004). Aquatic invertebrate assemblages of wetlands and rivers in the weatbelt region of Western Australia. Records of the Western Australian Museum 67, 7–37.
| Aquatic invertebrate assemblages of wetlands and rivers in the weatbelt region of Western Australia.Crossref | GoogleScholarGoogle Scholar |
Pinder, A. M., Halse, S. A., McRae, J. M., and Shiel, R. J. (2005). Occurrence of aquatic invertebrates of the wheatbelt region of Western Australia in relation to salinity. Hydrobiologia 543, 1–24.
| Occurrence of aquatic invertebrates of the wheatbelt region of Western Australia in relation to salinity.Crossref | GoogleScholarGoogle Scholar |
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41, D590–D596.
| The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.Crossref | GoogleScholarGoogle Scholar |
Raghukumar, S. (2017). ‘Fungi in Coastal and Oceanic Marine Ecosystems.’ (Springer International: Cham, Switzerland.)
Reed, J. (1998). A diatom-conductivity transfer function for Spanish salt lakes. Journal of Paleolimnology 19, 399–416.
| A diatom-conductivity transfer function for Spanish salt lakes.Crossref | GoogleScholarGoogle Scholar |
Rogerson, A., and Hauer, G. (2002). Naked amoebae (Protozoa) of the Salton Sea, California. In ‘The Salton Sea: Proceedings of the Salton Sea Symposium’, 13–14 January 2000, Desert Hot Springs, CA, USA. (Eds D. A. Barnum, J. F. Elder, D. Stephens, and M. Friend.) pp. 161–177. (Springer: Dordrecht, Netherlands.)
Skinner, R., Sheldon, F., and Walker, K. F. (2001). Propagules in dry wetland sediments as indicators of ecological health: effects of salinity. Regulated Rivers: Research and Management 17, 191–197.
| Propagules in dry wetland sediments as indicators of ecological health: effects of salinity.Crossref | GoogleScholarGoogle Scholar |
Snoeijs, P., and Weckström, K. (2010). Diatoms and environmental change in large brackish-water ecosystems. In ‘The Diatoms: Applications for the Environmental and Earth Sciences’. (Eds E. F. Stoermer and J. P. Smol.) pp. 287–308. (Cambridge University Press: Cambridge, UK.)
Stagg, C. L., Baustian, M. M., Perry, C. L., Carruthers, T. J. B., and Hall, C. T. (2018). Direct and indirect controls on organic matter decomposition in four coastal wetland communities along a landscape salinity gradient. Journal of Ecology 106, 655–670.
| Direct and indirect controls on organic matter decomposition in four coastal wetland communities along a landscape salinity gradient.Crossref | GoogleScholarGoogle Scholar |
Stat, M., Huggett, M. J., Bernasconi, R., DiBattista, J. D., Berry, T. E., Newman, S. J., Harvey, E. S., and Bunce, M. (2017). Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Scientific Reports 7, 12240.
| Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment.Crossref | GoogleScholarGoogle Scholar |
Stevenson, R. J., Pan, Y., and van Dam, H. (2010). Assessing environmental conditions in rivers and streams with diatoms. In ‘The Diatoms: Applications for the Environmental and Earth Sciences’. (Eds E. F. Stoermer and J. P. Smol.) pp. 57–85. (Cambridge University Press: Cambridge, UK.)
Ward, D. P., Petty, A., Setterfield, S. A., Douglas, M. M., Ferdinands, K., Hamilton, S. K., and Phinn, S. (2014). Floodplain inundation and vegetation dynamics in the Alligator Rivers region (Kakadu) of northern Australia assessed using optical and radar remote sensing. Remote Sensing of Environment 147, 43–55.
| Floodplain inundation and vegetation dynamics in the Alligator Rivers region (Kakadu) of northern Australia assessed using optical and radar remote sensing.Crossref | GoogleScholarGoogle Scholar |
Weston, N. B., Vile, M. A., Neubauer, S. C., and Velinsky, D. J. (2011). Accelerated microbial organic matter mineralization following salt-water intrusion into tidal freshwater marsh soils. Biogeochemistry 102, 135–151.
| Accelerated microbial organic matter mineralization following salt-water intrusion into tidal freshwater marsh soils.Crossref | GoogleScholarGoogle Scholar |
White, E., and Kaplan, D. (2017). Restore or retreat? Saltwater intrusion and water management in coastal wetlands. Ecosystem Health and Sustainability 3, e01258.
| Restore or retreat? Saltwater intrusion and water management in coastal wetlands.Crossref | GoogleScholarGoogle Scholar |
Whitehead, P. J., Wilson, B. A., and Bowman, D. M. J. S. (1990). Conservation of coastal wetlands of the Northern Territory of Australia the Mary River floodplain. Biological Conservation 52, 85–111.
| Conservation of coastal wetlands of the Northern Territory of Australia the Mary River floodplain.Crossref | GoogleScholarGoogle Scholar |
Williams, R. B. (1964). Division rates of salt marsh diatoms in relation to salinity and cell size. Ecology 45, 877–880.
| Division rates of salt marsh diatoms in relation to salinity and cell size.Crossref | GoogleScholarGoogle Scholar |
Woodroffe, C. D., Chappell, J. M. A., and Thom, B. G. (1986). ‘Geomorphological Dynamics and Evolution of the South Alligator Tidal River and Plains, Northern Territory.’ (North Australia Research Unit: Darwin, NT, Australia.)
Zhu, B. (2006). Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR). Water Research 40, 3231–3238.
| Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR).Crossref | GoogleScholarGoogle Scholar |
