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. 2016 Jun 21;3:160043. doi: 10.1038/sdata.2016.43

A database of marine phytoplankton abundance, biomass and species composition in Australian waters

Claire H Davies 1,a, Alex Coughlan 2, Gustaaf Hallegraeff 3, Penelope Ajani 4, Linda Armbrecht 5, Natalia Atkins 6, Prudence Bonham 1, Steve Brett 7, Richard Brinkman 8, Michele Burford 9, Lesley Clementson 1, Peter Coad 10, Frank Coman 11, Diana Davies 1,12, Jocelyn Dela-Cruz 13, Michelle Devlin 14, Steven Edgar 11, Ruth Eriksen 1,3, Miles Furnas 8, Christel Hassler 15, David Hill 7, Michael Holmes 16, Tim Ingleton 13, Ian Jameson 1, Sophie C Leterme 17, Christian Lønborg 8, James McLaughlin 18, Felicity McEnnulty 1, A David McKinnon 8, Margaret Miller 11, Shauna Murray 4, Sasi Nayar 19, Renee Patten 20, Tim Pritchard 13, Roger Proctor 6, Diane Purcell-Meyerink 21, Eric Raes 22, David Rissik 23, Jason Ruszczyk 24, Anita Slotwinski 11, Kerrie M Swadling 3,12, Katherine Tattersall 6, Peter Thompson 1, Paul Thomson 22,25, Mark Tonks 11, Thomas W Trull 1,12, Julian Uribe-Palomino 11, Anya M Waite 25,26, Rouna Yauwenas 4, Anthony Zammit 27, Anthony J Richardson 11,28
PMCID: PMC4915276  PMID: 27328409

Abstract

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.

Subject terms: Community ecology, Biodiversity, Marine biology

Background & Summary

Phytoplankton are microalgae at the base of the food web and directly or indirectly support all marine life. As highly efficient primary producers they are critical to maintaining biodiversity and supporting fisheries throughout the ocean1. Due to their high turnover rates and sensitivity to changes in environmental conditions phytoplankton are useful indicators of changing oceanographic conditions, climate change, and deterioration in water quality2,3. Some phytoplankton produce toxins which may be accumulated by filter feeding shellfish, causing irritation, serious illness or death to animals and humans.

A litre of seawater may contain up to one million algal cells, representing at least 100–150 different species4. These include the larger phytoplankton, dominated by the diatoms and dinoflagellates, but also include flagellates and the coccoid picoplanktonic forms. Currently, 537 infraspecific dinoflagellate and 938 diatom taxa are known to inhabit coastal and oceanic waters around Australia5,6. The fractions of nanoplankton flagellates and coccoid picoplankton, although smaller in size, can account for up to 90% of the total phytoplankton chlorophyll under low biomiass scenarios in offshore waters4. The latter are difficult, or impossible, to identify with light microscopy. Including a reliable estimate of biomass, along with cell abundance will provide more realistic information about the phytoplankton community structure at a particular point in time.

Many researchers have phytoplankton data sitting around on paper records or in spreadsheets, some published and some unpublished, which may eventually be lost or misplaced. Consultancies often hold data archives from several research projects from which data are released only to the client with no time and incentive to publish. These data, archived thoroughly, standardised and freely available to a wider audience, are an invaluable resource for the research community. Small, individual datasets with limited stand alone impact, can collectively provide valuable additions to large scale spatial and temporal studies. Many of these data have previously been published in some form. Journal articles, theses and reports and especially older publications, rarely include the relevant dataset so the data are not available for use after publication unless the author releases the data to a publically accessible platform. Even when data are released, they are often only presence data and are not explicit as they could be.

The Australian Phytoplankton Database has been collated from literature, active and retired researchers, consultancies, archives and databases (Fig. 1). Only data with the relevant corresponding metadata about collection location, date and methods has been included. Figure 2 shows the spatial extent of the records collected in this data set. Taxonomic identification of many phytoplankton taxa is fraught with difficulties, especially when limited to light microscopy. Whilst all have been standardised to the correct current classification as given by the World Register of Marine Species (WoRMS) (http://www.marinespecies.org/aphia.php?p=webservice), it is clearly not possible to verify every identification made by each analyst.

Figure 1. Flow diagram of data collation, verification and release to AODN.

Figure 1

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Figure 2. Locations of data for each project in the Australian Phytoplankton Database.

Figure 2

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The Australian Phytoplankton Database contains data on marine phytoplankton abundance, biomass and species composition. It can be used to:

  • develop distribution or biogeographic maps4,7;

  • determine community structures and range changes over time8,9 or oceanographic conditions10;

  • understand dynamics of harmful algal species to help inform the aquaculture industry11;

  • develop inputs to climate, ecosystem and fisheries models to inform management about resources12.

The Australian Phytoplankton Database is available through the Australian Ocean Data Network (AODN: http://portal.aodn.org.au) portal. This portal is the main repository for marine data in Australia. The Phytoplankton Database will be maintained in the CSIRO data centre and can be updated with new records, which will automatically upload to the AODN. Researchers wishing to submit new data should contact the corresponding author or the AODN. A snapshot of the Australian Phytoplankton Database as it is at the time of this publication has been assigned a DOI and will be maintained in perpetuity by the AODN (Data Citation 1).

The Australian Phytoplankton Database has been built with ease of use and minimising user error in mind. Therefore it provides the clean data at a level that requires minimal interpretation. The CSIRO database holds all the raw data, for example original species names and ambiguous records, from these datasets, and researchers can request further information from the corresponding author if required.

Methods

Samples were mainly collected from Niskin bottles, net drops or tows, and the Continuous Plankton Recorder (CPR). These are all standard methods of collecting phytoplankton samples13,14 and many are still largely reliant on a phytoplankton manual written in 1978 (ref. 15). A few samples were collected using automated samplers on moorings16. The sampling was done via research vessels, container ships and small boats by experienced researchers, students and volunteers. The majority of the samples were preserved using Lugol’s solution, although formalin, paraformaldehyde and glutaraldehyde have also been used. Different methods of preservation can affect the condition of the sample and which taxa are well preserved4,17. Samples were analysed with standard methods including light microscopy, transmission or scanning electron microscopy which are described in Hallegraeff, et al.4 All methodological variations within our phytoplankton database are detailed in the metadata where available and recorded for each data entry. Where available a citation is referenced for each project, which gives details on methodologies and limitations from that project (Table 1 (available online only)).

Table 1. Summary information on the project data sets, their location, time and taxonomic resolutions, numbers of samples and records available.

Project_id Project description Custodian (affiliation) Acknowledgement Location Start date End date No samples No records Taxonomic resolution
Organised by number of records (* ongoing datasets)                  
597* IMOS AusCPR14 Anthony Richardson (CSIRO) IMOS Australia 2007-12-17 2016-01-20 13866 1375559 Species where possible, zooplankton data available27
794* NSW Shellfish Program29,30 Steve Brett (Microalgal Services) Microalgal Services Estuaries in NSW 2004-08-24 2014-08-11 11669 1340327 HAB species only
1065* EPA VIC long term monitoring Renee Patten (EPA VIC) Microalgal Services Victoria 2008-02-21 2014-07-22 715 223266 Species where possible
599* IMOS NRS31 Anthony Richardson (CSIRO) IMOS Australia 2008-09-29 2015-12-12 490 95625 Species where possible, zooplankton and biogeochemical data available27
1054 Phytoplankton dynamics David Rissik (NCCARF)   Ballina NSW 1998-11-24 2000-11-27 407 93632 Species where possible
589 Bloom monitoring program Ian Jameson (CSIRO)   Tasmania 1992-10-12 1993-04-15 388 62076 Species of interest only
1051 Huon River sampling Peter Thompson (CSIRO)   Huon River TAS 1996-07-02 1998-10-05 1705 44517 Species where possible; chla
796 Phytoplankton zooplankton NSW9,10,32 Linda Armbrecht (Macquarie University) IMOS, OEH, NMSC Coffs Harbours NSW 2011-05-27 2012-09-12 297 44248 Species where possible, chla
1064* Hornsby Shire Council monitoring Peter Coad (Hornsby Council) Hornsby Council / Microalgal Services Hornsby area NSW 2003-05-06 2015-06-17 149 26969 Species where possible; chla
1068 GBR expedition 1928-29 Published literature   Great Barrier Reef QLD 1928-07-25 1929-07-17 462 33675 Species where possible
1066 Phytoplankton NW Shelf Miles Furnas (AIMS) GBRMPA North West Shelf WA 1997-10-26 2002-04-11 141 25803 Species where possible
807 Wet season phytoplankton Michelle Devlin (JCU)   North Queensland 2011-02-14 2014-05-17 206 25132 Species where possible
609 Phytoplankton dynamics Sophie C. Leterme (Flinders University)   Coorong Wetlands Gulf St Vincent SA 2010-07-01 2013-08-01 143 23171 Selected taxa identified to highest resolution possible
509 Gulf of Carpentaria phytoplankton33–35 Michele Burford (Griffith University)   Gulf of Carpentaria QLD 1986-05-08 1992-03-28 611 17856 Genera where possible
786 Voyage SS04/2007 Peter Thompson (CSIRO)   West Coast Australia 2007-05-16 2007-06-04 166 17264 Species where possible, chla
1056* SAIMOS moorings Sophie C. Leterme (Flinders University) IMOS South Australia 2010-07-01 2013-02-01 92 13858 Species where possible
479 Moreton Bay zooplankton floods Julian Uribe (CSIRO)   Moreton Bay QLD 2011-01-19 2011-12-21 84 12936 Species where possible, zooplankton data available27
1059 Continental Shelf Sophie C. Leterme (Flinders University)   East Coast Aus 2011-01-28 2013-07-31 208 12017 Selected taxa identified to highest resolution possible
806 Phytoplankton Great Barrier Reef Miles Furnas (AIMS) GBRMPA Great Barrier Reef QLD 1986-02-07 2001-08-28 88 11748 Species where possible
790 Voyage FR10/2000 Peter Thompson (CSIRO)   West Coast Australia 2000-11-15 2000-11-26 102 10608 Species where possible
1067 NW Shelf Phyto Paul Thomson (UWA) IMOS North West Shelf WA 2015-01-18 2015-01-24 46 8234 Species where possible
788 Voyage SS07/2005 Peter Thompson (CSIRO)   West Coast Australia 2005-07-21 2005-08-10 72 7488 Species where possible
784 Voyage SS08/2003 Peter Thompson (CSIRO)   West Coast Australia 2003-10-02 2003-10-21 57 5928 Species where possible
795 Perth Long Term Ocean Outlet Peter Thompson (CSIRO)   Perth 1999-03-24 2000-03-30 64 5687 Species where possible
1057 Phytoplankton from coastal lagoons in Sydney Shauna Murray (UTS)   Sydney NSW 2011-11-02 2014-05-02 259 5222 Species where possible
575 NOAA NOAA   Australia 1947-03-11 1984-02-16 138 4786 Species where possible
1058 Storm Bay Ruth Eriksen (IMAS)   Storm Bay TAS 2009-11-09 2015-04-22 85 4703 Species where possible; chla
801 PSP study Tim Ingleton (EnvNSW)   Morpeth NSW 2001-09-03 2001-11-12 87 3306 Species where possible, chla
780 World Ocean Database 200936 OBIS World Ocean Database 2009   Australia 1946-12-30 1984-02-16 118 2961 Species where possible
782 Phytoplankton Port Hacking 100 m station37,38 Penelope Ajani (Macquarie University)   Port Hacking NSW 1997-04-03 2009-12-07 113 2944 Species where possible, chla
559 Wood (1954).39 Published literature   Australia 1902-01-01 1955-01-01 33 2924 Species where possible
511 Crosby & Wood (1958).40 Published literature   Australia 1938-11-01 1958-01-01 32 2670 Species where possible
804 Solander cruise #5867 Diane Purcell-Meyerink (NAMRA & AIMS) NAMRA / AIMS Darwin & Van Diemen Gulf, NT 2013-09-09 2013-09-22 34 2530 Species where possible, chla
805* Southern Ocean Time Series Ruth Eriksen (CSIRO)   Southern Ocean Time Series mooring 2010-09-12 2011-04-07 24 2409 Species where possible
792 Voyage FRxx/2005 Peter Thompson (CSIRO)   West Coast Australia 1995-06-13 1995-06-14 23 2392 Species where possible
1070 Benthic dinoflagellates41 Michael Holmes (DSITI)   East Coast Queensland 1982-12-02 1990-02-28 889 2186 Selected genera only, units are no per g substrate
1053 SS voyages 2010-201342,43 Anya Waite (UWA/AWI)   West Coast Australia 2010-07-10 2013-07-21 255 2111 Genera where possible; chla
752 Icota—Pelagant Icota—Pelagant Icota—Pelagant   Australia 2004-01-19 2004-01-28 54 1749 Species where possible
1069 Voyage FR05/199544 Peter Thompson (CSIRO)   West Coast Australia 1995-06-04 1995-06-15 24 1562 Species where possible
800 Franklin voyage CTD Noctiluca scintillans45 Jocelyn Dela-Cruz (UNSW)   NSW 1998-11-14 1999-02-01 1046 1046 Noctiluca scintillans only
571 CSIRO (1965). Published literature   Port Hacking NSW 1965-04-14 1965-12-20 1 925 Species where possible
555 Rothlisberg & Pollard, et al. (1994).46 Peter Rothlisberg (CSIRO)   Gulf of Carpentaria 1988-01-01 1988-01-01 4 744 Genera where possible
778 Spring Phytoplankton Assemblages36 OBIS CLIVAR-SR3   Southern Ocean 2001-11-03 2001-12-10 751 751 Species where possible
799 Franklin voyage underway Noctiluca scintillans45 Jocelyn Dela-Cruz (UNSW)   NSW 1998-11-14 1999-01-30 504 504 Noctiluca scintillans only
573 Jeffrey & Carpenter (1974).47 Published literature   Port Hacking NSW 1971-09-01 1972-05-16 423 423 Species where possible
567 ANZ-DiatomsII Published literature   Australia and New Zealand 1844-01-01 1959-01-01 21 366 Species where possible
553 Revelante et al. (1982).48 Published literature   Australia     1 343 Species where possible
746 Diatoms from SAZ Sediment traps OBIS Diatoms from SAZ Sediment traps   Australia 1997-09-04 1997-09-20 3 304 Species where possible
1050 SS03/2010 Peter Thompson (CSIRO)   NW shelf WA 2010-04-16 2010-04-25 12 304 Species where possible
529 Hallegraeff & Jeffrey (1984).49 Gustaaf Hallegraeff (UTAS)   Australia 1980-06-08 1982-05-19 1 299 Species of interest only
803 Port Philip Bay50–52 Sasi Nayar (SARDI)   Port Philip VIC 2012-12-11 2012-12-13 9 297 Genera where possible
587 Hallegraeff’s notebook Gustaaf Hallegraeff (UTAS)   Australia 1982-07-05 1984-09-13 22 291 Species of interest only
537 Australian National Algae Culture Collection Ian Jameson (CSIRO)   Australia 1962-01-01 2008-01-01 24 288 Species of interest only
772 Ocean Drilling Program PANGAEA   Australia     11 264 Selected species only
766 International marine global change study PANGAEA   Australia     1 222 Species where possible
563 Wood (1961).53 Published literature   Australia 1961-01-01 1961-01-01 14 192 Species where possible
565 Wood, Crosby & Cassie (1959).54 Published literature   Australia 1875-01-01 1959-01-01 14 192 Species where possible
533 Hiramatsu & De Deckker (1996). Published literature   Southern Tasmania 1994-01-10 1994-01-10 5 185 Species where possible
768 Paleoenvironmental reconstructions PANGAEA   Australia     33 176 Selected species only
748 Electron Micrograph Database Electron Micrograph Database Electron Micrograph Database   Australia 1998-03-04 2005-03-03 45 165 Species where possible
541 Jeffrey & Hallegraeff (1987). Gustaaf Hallegraeff (UTAS)   Eddy Mario NSW 1981-05-01 1981-05-01 1 152 Species where possible
770 Deep Sea Drilling Project PANGAEA   Australia     8 134 Selected species only
543 LeRoi & Hallegraeff (2004). Gustaaf Hallegraeff (UTAS)   Australia 1994-06-01 1995-05-30 3 87 Species where possible
523 Hallegraeff (1984).55 Gustaaf Hallegraeff (UTAS)   Australia 1979-04-01 1984-01-01 7 84 Species of interest only
591 Zooplankton community dynamics Sarah Pausina (UQ) Healthy Waterways Moreton Bay QLD 2009-02-04 2011-09-28 82 82 Noctiluca Scintilans
527 Hallegraeff & Lucas (1988).56 Gustaaf Hallegraeff (UTAS)   Australia 1983-06-01 1988-01-01 6 81 Species of interest only
539 Jeffrey & Hallegraeff (1980).57 Gustaaf Hallegraeff (UTAS)   East Australian Current 1978-12-08 1978-12-08 1 79 Species where possible
802 Seagrass nutrient uptake studies58 Sasi Nayar (SARDI)   South Australia 2005-06-29 2006-02-27 9 75 Genera where possible
577 Wood (1963b).59 Published literature   Australia 1963-01-01 1963-01-01 7 65 Species where possible
545 LeRoi & Hallegraeff (2006).60 Gustaaf Hallegraeff (UTAS)   Tasmania Australia 1994-06-01 1995-05-30 3 58 Species of interest only
547 McMinn (1990).61 Published literature   Australia 1990-01-01 1990-01-01 9 58 Selected species only
569 CSIRO (1959). Published literature   Port Hacking NSW 1959-02-10 1959-12-15 1 51 Species where possible
585 Hallegraeff’s Coral Sea Notebook Gustaaf Hallegraeff (UTAS)   Coral Sea 1986-01-23 1986-02-02 49 49 Species of interest only
549 O’Connor et al (1996). Published literature   Macquarie Harbour NSW 1995-09-04 1995-09-04 1 45 Species where possible
758 MICROBIS database36 MICROBIS database   Australia     12 44 Selected species only
525 Hallegraeff & Reid (1986).62 Gustaaf Hallegraeff (UTAS)   Australia 1978-03-28 1979-04-30 1 32 Species of interest only
531 Hallegraeff & Jeffrey (1993).63 Gustaaf Hallegraeff (UTAS)   NSW and TAS 1981-10-01 1984-09-15 5 32 Species of interest only
551 Revelante & Gilmartin (1982).64 Published literature   Australia     1 32 Species where possible
581 CSIRO Voyage: SP3 Published literature   Australia 1982-03-09 1982-03-17 6 29 Species where possible
521 Hallegraeff (1983).65 Gustaaf Hallegraeff (UTAS)   Australia 1981-10-01 1982-03-01 1 28 Species of interest only
583 CSIRO Voyage: SP7 Published literature   Australia 1982-07-05 1982-07-05 4 24 Genera where possible
744 Diatom and foraminiferal samples36 OBIS (IOC)   Southern Ocean 1997-02-11 1997-02-11 1 21 Species where possible
517 Grant & Kerr (1970).66 Published literature   Port Hacking NSW 1966-04-01 1966-04-01 1 20 Species where possible
513 Cummins et al. (2004).67 Published literature   Tuggerah Lakes NSW 1999-01-01 1999-01-01 1 19 Genera where possible
515 Gottschalk et al. (2007).68 Published literature   Queensland 2007-01-01 2007-01-01 3 19 Species where possible
742 BOLD Marine Invertebrate Data36 OBIS BOLD Marine Invertebrate Data   Australia     12 17 HAB species only
519 Hallegraeff (1981).69 Gustaaf Hallegraeff (UTAS)   Port Hacking NSW 1978-01-01 1978-01-01 15 15 Species of interest only
579 CSIRO Voyage: G01 Published literature   Australia 1960-02-02 1960-02-04 2 12 Species where possible
764 Climate PANGAEA   Australia     9 9 One species only
754 Indian Ocean Node of OBIS OBIS IndOBIS—Indian Ocean Node of OBIS   Indian Ocean 1903-07-02 1930-07-02 1 6 Selected species only
756 JODC dataset JODC dataset   Australia 1977-06-28 1977-06-29 1 6 Species where possible
561 Wood (1963).70 Published literature   North West Australia 1963-01-01 1963-01-01 1 6 Selected species only
557 Thompson et al. (2008).71 Published literature   Huon River TAS 1997-01-01 2005-01-01 1 5 Selected species only
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There were three stages in data gathering. The first stage was to conduct a literature review of Australian phytoplankton data. Any literature that contained abundance or presence data was digitised and uploaded into the CSIRO maintained Oracle database. The second stage was to scan already existing databases, such as the CSIRO data trawler, the Ocean Biogeographic Ocean System (OBIS) and the Atlas of Living Australia (AOLA). These repositories only store presence records. Relevant data were selected and uploaded into the database. The third stage was to ask researchers to contribute any other data sets that they had. All data were organised into a standard format and uploaded into the database. Data were then served to and hosted by the AODN.

All taxa have been verified as accepted species and given the currently accepted name as defined by the World Register of Marine Species database (WoRMS—http://www.marinespecies.org/aphia.php?p=webservice). If any taxa could not be verified, then a second check was done through AlgaeBase (http://www.algaebase.org/). If this did not verify that taxa as a valid name then the taxonomic level of identification was decreased to a satisfactory level or the entry removed. All abundance values were standardised to cells.l−1 or are given as presence only. Records of the original identifications and units were archived so any records can be checked.

Identification of the smaller phytoplankton is often to a coarser taxonomic level as many cannot be distinguished to species using light microscopy. In some studies electron microscopy has been used to determine species, but in other studies functional groups have been identified. This data set does not include accessory pigment data which can help resolve these smaller taxa18 although it can be thought of as a complementary dataset. Over 20 years of pigment data are available in Australia via the AEsOP database (http://aesop.csiro.au/).

Cell biovolume is calculated as per Hillebrand, et al.19 following the suggested shape factors for each genera. Size parameters were estimated from measurements taken from Australian samples or Australian references where available4,20 and other sources where not21–23. In some data sets, direct measurements of size classes (e.g., P599 the Australian Continuous Plankton Recorder Survey and P597 the IMOS National Reference Stations), were used in preference to literature values. For some taxa there was insufficient information available to estimate a biovolume, these were generally the rare taxa. Rather than estimate a size class without any information available, these have been left blank.

Data Records

Each data record represents the abundance or presence of a phytoplankton taxa at a certain point in space and time and has been given a unique record identification number, P(project_id)_(sample_id)_(record_id). Each data record belongs to a project, with each project having a unique identification number, Pxxx. A project is defined as a set of data records which have been collected together, usually as a cruise or study with the same sampling method and having the same person counting the samples. Metadata ascribed to a project relates to all the data records within that project. Details to identify each separate project are given in Table 1 (available online only). Each sample within that project has a unique sample_id. The sample_id has not been changed from the original data set to maintain traceability. So these may be duplicated between projects but P(project_id)_(sample_id) will be a unique entity in space and time. Species abundance records within the sample are given a unique record_id.

The majority of these projects have been uploaded as part of the collation of data for this database. None have been previously published as datasets but The IMOS National Reference Stations, P599, and Continuous Plankton Recorder Survey, P597, which together constitute half the data in this database, are continually updated and available through the AODN (https://portal.aodn.org.au/search?uuid=dfef238f-db69-3868-e043-08114f8c8a94 and https://portal.aodn.org.au/search?uuid=c1344979-f701-0916-e044-00144f7bc0f4 respectively).

Table 1 (available online only) gives summary information on the project data sets, their space, time and taxonomic resolutions, numbers of samples and records available. Users can select data sets from this information and download as desired through the AODN.

Technical Validation

The Phytoplankton Database will provide an extensive resource for phytoplankton researchers, although there are some caveats due to the variety of the sampling and analysis protocols.

The various sample collection methods infer that abundances might not always be directly comparable across projects. For example, quantitative methods such as bottle sampling (e.g., Project 599) will collect all but the rarest phytoplankton and will include the whole size spectrum, whereas semi-quantitative methods such as net sampling are selective and dependent on tow method, mesh size and the mix of species present in the water as some species may clog the net and trap smaller species that would otherwise go through the mesh (e.g., Project 509)21. By including all data collected using different methods and including this information as meta-data, researchers are able to analyse the relative abundance of each taxa within a project and compare across compatible projects. Metadata includes as much detail as is available about sampling methods and limitations and provides guidance to the users about the potential of each data set. Users should consider collection methods, preservation techniques and microscopic limitations when comparing datasets. All datasets have been standardised to taxa/m3 of water except P1070 where the units are taxa per gram of substrate measured. This project collected the phytoplankton by collecting substrates and analysing parts of the substrate. It is included here as the only data set on Gambierdiscus and associated benthic dinoflagellates from Australia which are important to the studies of the ciguatera.

All datasets submitted can be interpreted as confirming the presence of those species recorded. In some datasets, e.g., time series, it is possible also to infer absences, assuming that all species are looked for on each sampling occasion. Absences have been included in the data sets where the project information available allowed us the confidence to interpret such absences correctly. The interpretation of absences from other projects is at the discretion of the user. We suggest that a project-by-project approach should be taken. If a taxa is not observed at all in a project, then the absence could be due to the taxa not being present, that taxa not being of interest to the analyst, or the inability to identify that taxa. Thus, a real absence should not be inferred. If a taxa is observed in some samples of a project, it can most likely be assumed that the microscopist could identify the taxa, and that a real absence may be inferred in samples within that project where the taxa was not marked as present.

Some data records were removed when there was ambiguity as to the identification of the taxa, i.e., when the taxonomic traceability, usually from older sources, was confused or when spelling mistakes make it unclear which one of two species was meant. Species known as freshwater species were removed as the methods used to collect data were not aimed at freshwater environments and the inclusion of the odd records of these species would not be comprehensive or meaningful. Estuarine species were captured and the records kept. Data records with positions on land, with an unreal number for abundance or with impossible dates were also removed or converted to presence records.

Usage Notes

The database contains information on the functional group of the species, which can aid analysis. Functional groups include diatoms, dinoflagellates, flagellates, ciliates (including tintinnids), silicoflagellates, and cyanobacteria. Once downloaded and binned as required, data are suitable for use in the creation of ecological indicators. For example:

  • Total diatoms, dinoflagellates

  • Diatom:Dinoflagellate ratio

  • Total phytoplankton abundance or biomass per degree square

Abundance (cells.l−1) for the phytoplankton counts is given where it is available, providing more information about the productivity of an area than presence data alone. A low cell abundance may indicate a low level or production, but this may not be the case if these are large cells. The biomass data helps to show productivity of an area. The biovolume has been calculated for each cell count and when converted to biomass, is available for use by modellers and to assist in interpretation of an area’s productivity. An accepted method of converting biovolume to biomass is to assume that the cell has the density of water (1 mm3.l−1=1 mg.l−1)13. Another useful conversion is to carbon biomass; full methods are readily found in the literature24–26. Table 2 gives details conversions of phytoplankton size data to carbon biomass.

Table 2. Information for converting biovolume V (μm3) to carbon biomass B (pgC.cell−1).

Group Equation
Diatoms24 B=0.288×V0.811
Dinoflagellates24 B=0.76×V 0.819
Tintinnids25 B=444.5+0.053×V
Ciliates24 B=0.22×V 0.939
Other protists24 (excluding diatoms) B=0.216×V 0.939
Silicoflagellates as for diatoms
Phaeocystis antarctica26 Use B=9 pg C cell−1
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Some of the data records are missing dates or coordinates. It was considered useful to keep these records as the presence of a taxa in a location may still be of value. The user may estimate coordinates from the location given and would then also be aware that these would not be the exact coordinates of the sample.

Data can be analysed in many different ways and in many software applications (e.g., R, Matlab). We include here some figures created in The R Project for Statistical Computing (https://www.r-project.org) to demonstrate some potential uses of the data (Fig. 3).

Figure 3. Demonstrated uses of phytoplankton data in the Australian Phytoplankton Database.

Figure 3

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(a) Map showing the range extension of Noctiluca scintillans over the past 150 years28; (b) Parameterisation of an ecosystem model (Atlantis) of diatom abundance using satellite chlorophyll Phytoplankton Functional Type analysis and the Continuous Plankton Recorder species ratios; (c) Diatom diversity by latitude from the Continuous Plankton Recorder; (d) Distribution of potentially harmful algal bloom species Dinophysis tripos.

In some cases, notably project 599, the IMOS National Reference Stations, the phytoplankton component of the survey is only a part of the data available. Additional biogeochemical data are available for this data set via the AODN. Some of the projects, viz. P479, P599, P597, have corresponding zooplankton data freely available in The Australian Zooplankton Database27. These data sets can be matched by the project_id and the sample_id which are consistent across databases. The list of citations referenced in Table 1 (available online only) will also give users information as to how this data has been previously used from the discrete projects.

Additional information

How to cite this article: Davies, C. H. et al. A database of marine phytoplankton abundance, biomass and species composition in Australian waters. Sci. Data 3:160043 doi: 10.1038/sdata.2016.43 (2016).

Supplementary Material

sdata201643-isa1.zip (10.6KB, zip)

Acknowledgments

We acknowledge the contributions from all collaborators and their institutions. If data from multiple projects are used, please acknowledge this publication; if individual project data are used, please acknowledge use of data as per the custodian information. We would also encourage the data user to enter into collaboration with the researchers involved in the data they use—understanding the history of a project will add value to the research. The relevant acknowledgement data is available from the metadata files attached to the data.

If using data from Project 599 the National Reference Stations or Project 597 the Australian Continuous Plankton Recorder, please use the following acknowledgement:

‘Data sourced from the Integrated Marine Observing System (IMOS)—IMOS is a national collaborative research infrastructure, supported by the Australian Government.’

Similarly for Projects 806 and 1066, please use the following acknowledgement:

‘A part of the data included in the database was obtained with support from the Great Barrier Reef Marine Park Authority, through funding from the Australian Government Reef Program and from the Australian Institute of Marine Science’.

Footnotes

The authors declare no competing financial interests.

Data Citations

  1. Davies C. H. 2016. Australian Ocean Data Network. http://dx.doi.org/10.4225/69/56454b2ba2f79

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Citations

  1. Davies C. H. 2016. Australian Ocean Data Network. http://dx.doi.org/10.4225/69/56454b2ba2f79

Supplementary Materials

sdata201643-isa1.zip (10.6KB, zip)

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