Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria
Antonie van Leeuwenhoek
Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria
0 I. C. Sutcliffe (&) Faculty of Health and Life Sciences, Northumbria University , Newcastle upon Tyne NE1 8ST , UK
1 M. E. Trujillo Departamento de Microbiolog ́ıa y Gene ́tica , Edificio Departamental , Lab, Universidad de Salamanca , 214, Campus Miguel de Unamuno, 37007 Salamanca , Spain
2 R. Rossello ́-Mo ́ra Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avanc ̧ats (CSIC-UIB) , E-07190 Esporles, Balearic Islands , Spain
It is self-evident that contemporary biological science has become a database-driven endeavour, ranging from databases serving broad communities (such as Genbank) to those that are more specialised. We have argued previously (Rossello´-Mo´ ra 2012; Sutcliffe et al. 2012) that it would greatly benefit Archaeal and Bacterial systematics to create an iterative taxonomic database of Archaeal and Bacterial species, which would provide a summative and evolving repository for information on species characteristics, such as those typically found in the protologues of descriptions of novel genera and species. Indeed, such a database would be a welcome complement to MycoBank, a comparable initiative in fungal taxonomy (Robert et al. 2013), and important databases of microbial nomenclature and identification such as
-
LPSN, LTP and EzTaxon
(Yarza et al. 2010; Parte
2014; Yoon et al. 2017)
.
As Editors of Antonie van Leeuwenhoek and
Systematic and Applied Microbiology, we are
responsible for two journals that effectively publish the
descriptions of significant numbers of Archaeal and
Bacterial species. Given the importance of getting a
database established, we have therefore developed a
‘digital protologue’ database (DPD) to accompany
descriptions of novel Archaeal and Bacterial taxa
published in these two journals. Having been tested by
volunteer authors, we believe the DPD has good
functionality and fitness for purpose as a repository for
taxonomic data, and we expect to refine and improve
its design and interactivity in response to feedback
from users. Significant features include accession
numbers to relevant sequence databases (which will
become still more important as whole genome
sequences increasingly accompany descriptions of
novel microbial taxa) and the generation of unique
TaxoNumbers for each entry (which can also be cited
and used for microattribution purposes). Moreover,
content is exportable in a tabulated format that can be
used as Online Supplementary material to accompany
published material. At present the database is focussed
on descriptions of Archaeal and Bacterial species
although options are available to create entries for the
description of genera and Candidatus taxa. As the
current version will no doubt evolve, we encourage all
users to feed-back to the editors for improvements.
From March 2017, the Editors of Antonie van
Leeuwenhoek and Systematic and Applied
Microbiology will require all descriptions of novel Archaeal and
Bacterial taxa to be accompanied by a mandatory
entry in the DPD and to include a TaxonNumber
(similar to current policy regarding deposition of
information on novel fungal taxa in MycoBank). In
time, we also hope the systematics community will
also help enter data on previously described taxa (e.g.
the current nearest phylogenetic relative) in order to
‘backfill’ the database. The DPD will be curated by
relevant Editors of the journals that encourage authors
to submit entries and will be editable to ensure updates
(for example, as names move from being ‘effectively
published’ to ‘validly published’). In time, we hope to
encourage the participation of other journals to allow
the DPD to grow into a long overdue cumulative and
authoritative database of the characterised Archaeal
and Bacterial world.
It is highlighted that this Editorial text is being
simultaneously published in Antonie van
Leeuwenhoek and Systematic and Applied Microbiology.
Availability The DPD is available at http://imedea.
uib-csic.es/dprotologue/.
Acknowledgements We are very grateful to Tolo Mir for
excellent technical assistance in developing the DPD, to Barny
Whitman for constructive discussions and to the volunteer
taxonomists who helped beta-test and feedback on early
prototypes of the DPD.
Parte AC ( 2014 ) LPSN-list of prokaryotic names with standing in nomenclature . Nucleic Acids Res 42 : D613 - D616
Robert V , Vu D , Amor AB , van de Wiele N , Brouwer C , Jabas B , Szoke S , Dridi A , Triki M , Daoud SB , Chouchen O , Vaas L , de Cock A , Stalpers JA , Stalpers D , Verkley GJM , Groenewald M , Borges dos Santos F , Stegehuis G , Li W , Wu L , Zhang R , Ma J , Zhou M , Pe´rez Gorjo´n S , Eurwilaichitr L , Ingsriswang S , Hansen K , Schoch C , Robbertse B , Irinyi L , Meyer W , Cardinali G , Hawksworth DL , Taylor JW , Crous PW ( 2013 ) MycoBank gearing up for new horizons . IMA (...truncated)