What is the MapApp and how does it work?
A web application that can be used to map global microbial abundance. It has a set of ASVs (Amplicon Sequence Variants) of 16S and 18S rDNA genes from microbial communities sampled during the Malaspina expedition. After a request, it will identify all ASVs matching the query and create a map displaying their relative abundance at the surface and along vertical profiles. Depending on the database you may perform queries using 16S/18S rDNA sequences, taxonomic classifications or sequence identifiers.
Can I use my own OTU/ASV tables?
Yes you can. If you register and verify your email address, you get the option of creating your own database with your own data. The only requirements are that you use CSV files (no quotes), with one of the applicable separators, and have the correct headers (column names) in your files. More details are available on the user dashboard panel, used to upload DBs.
Can I download the results?
Yes! Each layer of the map is individually downloadable as an SVG file, which can be further edited with vector graphics programs such as Inkscape or Illustrator, and easily converted into publication quality graphics.
In addition you can download the depth profiles (given as PNG files), and the BLAST results, coordinates of the matched sampling stations, taxonomic profiles (if provided in the DB) by going to the “Download” tab.
Can I compare multiple sequences?
Yes! The dropdown at the top of the page is the results list. You can use it to switch between different matching hits (if performing BLAST), you can compare the distribution of the individual sequences by choosing one and clicking ‘Compare’.
This will plot a separate layer of circles, colored blues, a bit to the south of their actual position, in order to allow you to compare two sequences simultaneously. You can remove them by clicking on the ‘reset view’ button.
Can I add new results to a comparison?
Yes! After performing an initial query you can go to the bottom of a results page, and there you will find the “Compare” section, where you can choose the parameters for a new search.
This will lead you to a new results page where the results from the new query will be added to the dropdown above the map. From here you can select your new results, and by clicking the “Compare” button the new results will be laid out in front of you. This is useful for situations where you are using taxonomies or sequence names for comparisons, as those results only have a single result.
Details about the build-in databases
16S ASVs from the Malaspina-2010 expedition - Prokaryotes
- MalaSurf: Surface samples; DNA extracts. Picosize fraction (0.2-3.0 µm). Ruiz-González et al. 2019 (https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15026)
- MalaDeep: Bathypelagic samples; DNA extracts. Picosize fraction (0.2-0.8 µm). Salazar et al. 2016 (https://www.nature.com/articles/ismej2015137)
- MalaSizeFrac: Vertical profiles; DNA extracts. Picosize fraction (0.2-0.8 µm). Mestre et al. 2018 (https://www.pnas.org/content/115/29/E6799.short)
18S rDNA ASVs from the Malaspina-2010 expedition - Eukaryotes
- MalaSurf: Surface samples; DNA extracts. Picosize fraction (0.2-3.0 µm). Logares et al. 2020 (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00827-8)
- MalaVP: Vertical profiles; DNA and RNA samples. Picosize fraction (0.2-3.0 µm). Giner et al. 2020 (https://www.nature.com/articles/s41396-019-0506-9)
Methodological details for rDNA databases
Environmental DNA and RNA was extracted as indicated in the corresponding publications. Prokaryotic 16S rRNA genes (V4-V5 region) were amplified with primers 515F-Y - 926R, while eukaryotic 18S rDNA genes (V4 region) were amplified with TAReukFWD1 and TAReukREV3. Amplicon libraries were paired-end sequenced on an Illumina MiSeq platform (2x250bp). Raw sequences were clustered to Amplicon Sequence Variants (ASVs) by DADA2 with parameters truncLen 220,200, maxEE 2,4 for prokaryotes and truncLen 220,210, maxEE 6,8 for eukaryotes. For prokaryotes, ASVs were assigned taxonomy using the naïve Bayesian classifier method together with the SILVA 132 database. Chloroplasts and mitochondria were removed and the ASVs table was rarefied to 20,000 reads per sample. For eukaryotes, samples with less than 800 reads were removed, as well as ASVs present in only 1 sample with less than 10 reads. Taxonomic assignment of V4 ASVs was performed using the in-house eukaryotesV4 database (https://github.com/aleixop/eukaryotesV4). ASVs associated to Nucleomorph, Metazoa and Charophyta were discarded, and relative abundances of OTUs in each sample were obtained as percentages.
Something is not working/weird.
If you run into any issues please send an email with the URL of your analysis to firstname.lastname@example.org and we will take a look.