Nannotax: a web taxonomy resource for nannoplankton research, training and reference

Lead Research Organisation: University College London
Department Name: Earth Sciences

Abstract

Coccolithophores are single-celled, marine algae (phytoplankton), which produce elaborate calcite scales (coccoliths) that form a protective covering around their delicate cell walls. They are an important part of the modern marine ecosystem, but also have a long fossil record (nannofossils) stretching back 225 million years (Triassic). Both living and fossil coccolithophores provide valuable information about ocean environments and changing climate. The fossils also provide a simple and quick means of age-dating the rocks in which they are found. For these reasons, coccolithophores are of interest to a very wide range of scientists, including marine biologists, palaeoceanographers and geologists (stratigraphers). The effective use of coccolithophores is dependent upon the availability of up to date and reliable information concerning their classification (taxonomy - which species is which, and why?), their ecology (which species live where, when and why?) and their geological history (which species lived when and where?). However, this information is frequently difficult to find because it is dispersed throughout specialist publications. In order to widen access to this crucial information, we have started work on a web resource called Nannotax (www.nannotax.org) that we hope will become the online reference source for anyone needing to obtain basic to specialist information on coccolithophores and nannofossils. Our pilot version focused on the relatively recent, Neogene, fossil record (0-23 million years ago) and has already proved popular, registering 670,000 page views and 275 registered users. We now aim to build on this, and will add more species (the older fossil record, plus all the living species), add more types of data (age, ecology and, where appropriate, biology), expand the content (glossary, guides to identification and methods of study) and bring the site to the attention of those who will most benefit from it. The end-product Nannotax website will provide a complete listing of living and fossil coccolithophore and nannofossil taxa, with short descriptions, age data, multiple illustrations, bibliographic references and original descriptions. There will be identification keys and linked pages providing information on study methods. In parallel, we will provide hands-on training in the use and potential of the system, and respond to requests from those who have 'test-driven' the system at workshops and conferences. We think that the development of this system is essential to the hydrocarbon industry and to academics and educators involved in nannoplankton research, training and learning. By removing the barriers to learning nannoplankton taxonomy, identifying specimens and obtaining accurate information about species, existing users will be enabled to expand their expertise, and we believe it will also attract a range of new users. To ensure that we are providing the right kind of information for this wide range of scientists, we have enlisted the support of project partners who represent international biologists, oceanographers, geologists and oil company stratigraphers, who will both provide us with data, and also review and comment upon our progress and product.

Planned Impact

We believe that development of this system is essential to the hydrocarbon industry and to academics involved in nannoplankton research, training and learning, and this is backed up by our Project Partner letters. By lowering the barriers to learning taxonomy, identifying specimens and obtaining accurate information on taxa, existing users will be enabled to expand their expertise and we will be able to broaden the community of users. Indeed, making this breadth of data readily available is an untried experiment for micro-organisms, and we hope it will attract an interesting range of new users. However, some specific categories of users who will definitely benefit include:

Industrial biostratigraphers - Nannofossil biostratigraphy is a widely used tool in hydrocarbon exploration, and biosteering of horizontal wells has resulted in significant new recruitment of junior nannofossil biostratigraphers. Typical recruits have only limited taxonomic expertise, and training them is a real challenge for the sector. The currently-available Nannotax content is already being used for this, and the extended content will greatly increase the ability of novice biostratigraphers to rapidly expand their expertise.

Palaeoceanographers - Nannofossils are extensively used in palaeoceanography studies, both to provide a time-framework for the research (biostratigraphy) and for interpretation of environments and ecology. This work requires accurate identifications, but palaeoceanographers, especially MSc and PhD students, also have to learn many other skills and no longer have the time to undertake extensive taxonomic literature research. By making authoritative taxonomic data readily available, Nannotax will make nannofossil-based palaeoceanography much more practicable.

Plankton biologists and oceanographers - In this area, as in palaeoceanography, taxonomy is no longer an arcane art, of interest only to a limited set of experts, but rather a basic tool needed for a wide range of climate change, population biology, biogeochemical and molecular genetic studies. Nannoplankton identification is not intrinsically difficult, and through Nannotax we will make it accessible to any interested researcher or student.

In summary, Nannotax will make authoritative information on nannofossil and extant coccolithophore taxonomy readily accessible, and we anticipate that it will result in a significant increase in the volume and quality of pure and applied studies of this key group. We also believe that it will raise the benchmark for online availability of data on other microfossil and plankton groups, and so stimulate further online resources.

Publications

10 25 50
 
Description Microfossils are tiny fossils that can only be studied using microscopes but they are extremely abundant in sedimentary rocks (thousands to billions in very small samples), easy to identify, and evolved rapidly through time, regularly appearing or disappearing in the stratigraphic record. This means they can be used to divide up geological time (they are good 'index' fossils) and to reliably date sedimentary rocks, a requirement that is central to the Earth Sciences both in research and industry (e.g. oil and gas exploitation). However using microfossils as age-dating tools requires high-quality data on the stratigraphic age range of taxa, a global understanding of their biogeographic distribution, and a comprehensive and rigorous taxonomic classification framework. We have developed Nannotax (http://www.mikrotax.org/Nannotax3/), to provide basic to specialist information on the nannoplankton microfossil group. The core of the website currently consists of 2700 taxon pages each of which gives authoritative data on the nomenclatural taxonomy of the taxon, combined with a diagnosis, references, biostratigraphic data, additional notes (most cases) and images (for almost all taxa). The site is illustrated with ca 13,000 images including many high-resolution SEM images and colour light micrographs. In addition there is a catalogue of 5500 scanned pages of original descriptions, fully linked to main pages and 500 taxon pages covering non-coccolithophores.
This is now by far the best online resource for living or fossil coccolithophore taxonomy and to the best of our knowledge it is substantially better than anything available for other microfossil groups or extant microplankton groups. This reflected in usage statistics, e.g over the 6 months period 5th May to 5th November 2014 there have been around 255 thousand pages views with average duration of 13 minutes showing that visitors are making real use of the site, also reflected in the fact that 80% of visitors are returning users. The strong weekly cyclicity indicates that the site is primarily used as a working tool with weekend use minimal; there is also a noticeable decline in use during the summer university vacation months.
Exploitation Route The website design could be used to present similar kinds of information very easily. We have recently been funded to produce another online taxonomy resource for a second major microfossil group, planktonic foraminifera, and the results of this funding can be found at http://www.mikrotax.org/pforams/index.html
Sectors Digital/Communication/Information Technologies (including Software),Education,Energy,Environment,Culture, Heritage, Museums and Collections

URL http://www.mikrotax.org/Nannotax3/
 
Description The Nannotax project is primarily knowledge exchange and impact related. We have taken research-sourced taxonomic and biostratigraphic data and made it available as a web resource in collaboration with industrial project partners. The widespread use of the website is evidenced by Google Analytics and includes widespread use in the hydrocarbon exploration industry. http://ina.tmsoc.org/Nannotax3/index.php?dir=Coccolithophores
First Year Of Impact 2013
Sector Education,Energy,Environment
Impact Types Economic

 
Description NERC Innovation Grant
Amount £99,000 (GBP)
Funding ID NE/N017900/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2016 
End 03/2018
 
Title nannotax database 
Description The nannotax database is a curated taxonomic database providing an authoritative synthesis of the taxonomy of extant and fossil coccolithophores and other calcareous nannofossil, including >3000 taxa. Data includes >20,000 identified images with full metadata (stratigraphic and location data) and a full database of taxonomic ranges. The database is also linked to the Neptune database of occurrence records from the International Ocean Discovery Program and its precursors (Neptune data is displayed on the Nannotax website and Nannotax taxonomy is used in the Neptune database, and to the TimeScale Creator project (TSC age models are used on the Nannotax website and links to Nannotax are used on TSC as a source of reference data on nannofossils) 
Type Of Material Database/Collection of data 
Year Produced 2013 
Provided To Others? Yes  
Impact The database is primarily available via the nannotax website as a source of taxonomic data for use as a reference and training tool. Increasingly, however, the site and the underlying database is gaining value as a synthetic data source for research, and we are developing collaborations in this direction. 
URL http://www.mikrotax.org/Nannotax3
 
Title pforams@mikrotax 
Description Pforams@mikrotax is an online taxonomic database of planktonic foraminifera. It aims to provide a comprehensive source of information for industrial and academic scientists needing information on planktonic foraminifera species. It provides tools to help identify species or to look up the characteristics of species. Coverage includes data on original descriptions of ca 2500 taxa, and on modern taxon concepts for ca 1150 taxa. It is illustrated by ca 6000 images (most with 3 subimages). Features of the database include advancd search using morphological characters &/or geological time interval; plotting of occurrence-frequency data from the Neptune database; plotting of evolutionary trees. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The database has now become the standard online reference source for the field, with >100 users per day (source Google Analytics). 
URL http://www.mikrotax.org/pforams/index.html
 
Title mikrotax taxonomy content management sytem 
Description Mikrotax is a system to deliver taxonomic information on microfossils via the web. It is based on a combination of MySQL database, animate collection, php program and javascript functions. It is based on the system developed for the nannotax website but has been greatly enhanced during the follow-on planktonic foraminfera @ nannotax project. Specifically the system has been developed within the follow-on project to be a robust web-application which allows content to be developed by collaborating user-editors via the web. In addition the system is being developed to act as broader hub for integrating data on these microfossils especially through collaboration with the researchers in Berlin to integrate data from deep-sea drilling (Neptune project with data from DSDP, ODP, IODP). 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact The prime impact has been enabling the pforams@mikrotax site to be developed and to allow a team of user-editors from the USA (Smithsonian Institute) and Italy (Milan University) to develop and maintain a major part of the site. In addition the software is now available for other users and we are investigating potential further applications - including with calcareous dinoflagellates, acritarchs, radiolaria and pteropods. 
URL http://www.mikrotax.org
 
Description Conference organisations 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Lyell Meeting 2016 at the Geological Society - Palaeoinformatics: Synthesising data from the past to illuminate the future

Organised by Dr. Jeremy Young and building on (and reporting) the outputs from this research grant
Year(s) Of Engagement Activity 2016
URL https://www.geolsoc.org.uk/lyell16
 
Description Participation in INAsset nannofossil taxonomy summer school, Lyon 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The INAsset summer school in nannofossil taxonomy and stratigraphy was held in July 2018 in Lyon. I was invited to lecture on use of the Nannotax system, as well as on aspects fo my other research. In addition the website was used extensively throughout the week-long workshop.
Year(s) Of Engagement Activity 2018
URL http://ina.tmsoc.org/meetings/summerschool2018/inasset2018.html