The MicroEcoSystems Interaction database was assembled January through November 2017. Papers used to document interactions are published between 1894 and 2017. The search strategy to find the relevant literature and the template for organizing the database was done according to the Tara oceans projects similar effort in Lima-Mendez et al. (2015).
Initially, reviews resulting from the boolean search string (plankton* AND (marin* OR ocean*))
AND (parasit* OR symbios* OR mutualis*) in Scopus (https://www.scopus.com/) and Web of Science (http://webofknowledge.com/) were examined and the references therein further explored. In addition, literature on protist predation on other protists and bacteria were also screened.
This literature search strategy, followed by meticulously reading papers and included references,
was the main method for collecting papers documenting interactions. The database of screened literature from Lima-Mendez et al. (2015) was used as template to organize our database. The the two databases (Tara and MicroEcoSystems) were merged together and duplicate entries were removed.
Finally, entries from the AquaSymbio database (http://aquasymbio.fr/) were used to find papers not included in the initial literature search.
The database documents the ecological interaction between two organisms, identified down to the species level, if possible. Interactions are identified as parasitism, predation, benevolent symbiosis (either mutualism or commensalism) and unresolved interactions. Parasitism is used in cases where the paper at hand clearly underscores a parasitic interaction. Cases of kleptoplasty together with classical predation are contained within the group of entries termed predation. Symbiosis includes endo- and ectosymbiosis and is categorized into the different forms of symbiosis (e.g. photosymbiosis). Unresolved interactions are associations where it is uncertain whether the interactions are beneficial or antagonistic to the involved partners.
In addition to genus and species level, the taxonomic classification consists of three levels chosen pragmatically
to make the database more user friendly and portable. The highest level distinguishes between eukaryote and prokaryote taxa.
The second level places each taxon within super groups or other high taxonomic levels (e.g. Rhizaria or Alveolata)
following the scheme of (Adl et al. 2012). The third level places each taxon in larger groups below the supergroup taxonomic levels
(e.g. Ciliophora, Dinoflagellata and Acantharia). Each level of taxonomic names follows the nomenclature of the
Silva database (release 128, May/June 2017) (Pruesse et al. 2007; Yilmaz et al. 2014; Quast et al. 2013).
Species names have been updated to the most recent agreed upon classification in the database can therefore deviate
from the original papers they stem from are therefore not the same as the entries in the database due to several cases of synonymization.
The database also documents the methods used to determine the interacting species. Symbionts and/or hosts determined by any form of
microscopy or direct observation are denoted 1. Symbionts and/or hosts determined by sequencing or FISH are denoted 2.
The combination of the former two is denoted 3. Most interactions with observation type 2 also have accession numbers from GenBank (Benson et al. 2005) that are included in the database.
A published paper is associated to each interaction entry. When a DOI is available, it is included in the database.
Only interactions from aquatic systems are included (marine, brackish and freshwater).
The resulting database contains 2,448 entries from 534 publications.
PIDA is published in ISME: https://www.nature.com/articles/s41396-019-0542-5
1 = symbiont and/or host determined by direct observation (e.g. light microscopy , SEM )
2 = symbiont and/or host determined by molecular methods (e.g sequencing or FISH)
3 = both 1 and 2
Prot = Protist
Bac = Bacteria
Arc = Archaea
Protist is here defined as unicellular eukaryotes
Type of interaction as described in the original paper:
- Parasitism
- Predation
- Different forms of benevolent symbiosis (e.g. photosymbiosis, nitrogen-fixation and vitamin exchange)
- Unresolved interactions
If sequencing was applied in the study (on one or both organisms), and published in Genbank, accession number is included in the database
Org 1 = host
Org 2 = symbiont
Tax 1 = Eukaryote or prokaryote
Tax 2 = Supergroup or other high taxonomic level (e.g. Rhizaria, Alveolata, Metazoa)
Tax 3 = Larger groups below supergroup taxonomic level (e.g. Ciliophora, Dinoflagellata, Acantharia)
Taxonomic names (any level) follows the nomenclature of the Silva database. Taxonomic names used in articles may therefore not be identical to database entries as several species have synonyms.
Author and year of publication
DOI or other link to each reference
Either MicroEcoSystems or TARA
Unique identifier for each entry
Marine, brackish or freshwater
Information on the sampling: location, sampling method, culture, smaller scale habitat (e.g. sediment, surface water, etc.)
Bjorbækmo MFM, Evenstad A, Røsæg LL, Krabberød AK, Logares R. The planktonic protist interactome: where do we stand after a century of research? ISME J 2020; 14: 544–559.- Adl, Sina M., Alastair G B Simpson, Christopher E. Lane, Julius Lukeš, David Bass, Samuel S. Bowser, Matthew W. Brown, et al. 2012. “The Revised Classification of Eukaryotes.” Journal of Eukaryotic Microbiology 59 (5): 429–93. doi:10.1111/j.1550-7408.2012.00644.x.
- Benson, Dennis A., Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler. 2005. “GenBank.” Nucleic Acids Research 33 (DATABASE ISS.): 34–38. doi:10.1093/nar/gki063.
- Lima-Mendez, Gipsi, Karoline Faust, Nicolas Henry, Johan Decelle, Sébastien Colin, Fabrizio Carcillo, Samuel Chaffron, et al. 2015. “Determinants of Community Structure in the Global Plankton Interactome.” Science 348 (6237): 1262073. doi:10.1126/science.1262073.
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41 (D1): D590-D596.
- Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucl. Acids Res. 42:D643-D648.
- https://www.scopus.com/
- http://webofknowledge.com/
- http://aquasymbio.fr/
This data repository was configured to by indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org).