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DNA metabarcoding data: Altitudinal zonation of green algae biodiversity in the French Alps

Citation

Coissac, Eric et al. (2021), DNA metabarcoding data: Altitudinal zonation of green algae biodiversity in the French Alps, Dryad, Dataset, https://doi.org/10.5061/dryad.ksn02v746

Abstract

Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are key primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where alga have been shown to be major components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae can spread via airborne spores and settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of the vertical distribution in soils further highlighted the importance of pH and nitrogen/carbon ratios. This metabolic trait may also determine the Trebouxiophyceae over Chlorophyceae ratio. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in soil in mountain ecosystems, to comprehend the distribution of green algae species and dynamics in response to environmental changes.

Methods

The datasets correspond to DNA metabarcoding data produced following the protocol described in  article:

Altitudinal zonation of green algae biodiversity in the French Alps, 2021, Frontiers in Plant science (DOI: 10.3389/fpls.2021.679428).

The published data correspond to the alignment of forward and reverse reads using illumiinapairedends, demultiplexed by samples using ngsfiler, dereplicated using obiuniq and expunged of singleton sequences (sequences appearing only once in the complete data set) using obigrep.

The process of analysis is detailed at: https://alpalga.github.io/Zonation/

All scripts are available at: https://github.com/Alpalga/Zonation

Usage Notes

Data are FASTA formatted sequence files using the OBITools header convention for annotations. 
The analysis of the data can be facilitated using the  OBITools package http://mertabarcoding.org/obitools

Funding

Centre National de la Recherche Scientifique, Award: Mission pour l’Interdisciplinarité

Agence Nationale de la Recherche, Award: Alpalga ANR-20-CE02-0020

Agence Nationale de la Recherche, Award: Oceanomics ANR-11-BTBR-0008

Agence Nationale de la Recherche, Award: GlycoAlps ANR-15-IDEX-02

Agence Nationale de la Recherche, Award: GRAL Labex ANR-10- 1654 LABEX-04

Agence Nationale de la Recherche, Award: EUR CBS ANR-17-EURE-0003

Agence Nationale de la Recherche, Award: GlobNets ANR−16−CE02−0009

Agence Nationale de la Recherche, Award: AnaEE-France ANR-11-INBS- 1656 0001AnaEE-Services

Agence Nationale de la Recherche, Award: Montane, OSUG@2020 1658 ANR−10−LAB−56

Agence Nationale de la Recherche, Award: EUR CBS ANR-17-EURE-0003