W. Elbert, Contribution of cryptogamic covers to the global cycles of carbon and nitrogen, Nature Geoscience, vol.5, pp.459-462, 2012.

R. Ramanan, B. H. Kim, D. H. Cho, H. M. Oh, and H. S. Kim, Algae-bacteria interactions: Evolution, ecology and emerging applications, Biotechnology Advances, vol.34, pp.14-29, 2016.

M. Rippin, S. Lange, N. Sausen, and B. Becker, Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding, FEMS Microbiology Ecology, vol.94, pp.1-15, 2018.

S. V. Tesson, C. A. Skjøth, T. ?antl-temkiv, and J. Löndahl, Airborne Microalgae: Insights, Opportunities, and Challenges, Applied and Environmental Microbiology, vol.82, 1978.

S. Zancan, R. Trevisan, and M. G. Paoletti, Soil algae composition under different agro-ecosystems in North-Eastern Italy, Agriculture, Ecosystems and Environment, vol.112, pp.1-12, 2006.

F. Azam and F. Malfatti, Microbial structuring of marine ecosystems, Nature Reviews Microbiology, vol.5, pp.782-791, 2007.

P. M. Schenk, Second Generation Biofuels: High-Efficiency Microalgae for Biodiesel Production, BioEnergy Research, vol.1, pp.20-43, 2008.

L. Hoffmann, Algae of terrestrial habitats, The Botanical Review, vol.55, pp.77-105, 1989.

K. A. Palinska and W. Surosz, Taxonomy of cyanobacteria: A contribution to consensus approach, Hydrobiologia, vol.740, pp.1-11, 2014.

R. M. Soo, An expanded genomic representation of the phylum cyanobacteria, Genome Biology and Evolution, vol.6, pp.1031-1045, 2014.

J. S. Singh, A. Kumar, A. N. Rai, D. P. Singh, and . Cyanobacteria, A precious bio-resource in agriculture, ecosystem, and environmental sustainability, Front. Microbiol, vol.7, 2016.

L. A. Lewis, Chlorophyta on land: Independent lineages of green eukaryotes from arid lands, Algae Cyanobacteria Extrem. Environ, pp.569-582, 2007.

L. Pfister, Terrestrial diatoms as tracers in catchment hydrology: a review, Wiley Interdiscip. Rev. Water, vol.4, 1241.

M. Wanner, Soil Testate Amoebae and Diatoms as Bioindicators of an Old Heavy Metal Contaminated Floodplain in Japan, Microb. Ecol, vol.79, pp.123-133, 2019.

R. A. Andersen, Diversity of eukaryotic algae, Biodiversity and Conservation, vol.1, pp.267-292, 1992.

D. Bhattacharya and L. Medlin, Algal Phylogeny and the Origin of Land Plants, Plant Physiology, vol.116, pp.9-15, 1998.

O. Clerck, K. A. Bogaert, and F. Leliaert, Diversity and Evolution of Algae, Genomic Insights Into the Biology of Algae, vol.64, 2012.

P. J. Keeling, Diversity and evolutionary history of plastids and their hosts, American Journal of Botany, vol.91, pp.1481-1493, 2004.

F. Leliaert, Phylogeny and Molecular Evolution of the Green Algae, Critical Reviews in Plant Sciences, vol.31, pp.1-46, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01590252

R. L. Lowe and G. D. Laliberte, Benthic Stream Algae: Distribution and Structure, Methods in Stream Ecology: Third Edition, vol.1, 2017.

A. E. Pipe and L. E. Shubert, The use of algae as indicators of soil fertility. Algae as Ecological Indicators, pp.213-233, 1984.

T. Sauvage, W. E. Schmidt, S. Suda, and S. Fredericq, A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA, BMC Ecology, vol.16, pp.1-21, 2016.

M. Hügler and S. M. Sievert, Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean, Annual Review of Marine Science, vol.3, pp.261-289, 2011.

M. Muñoz-rojas, Cyanobacteria inoculation enhances carbon sequestration in soil substrates used in dryland restoration, Science of the Total Environment, vol.636, pp.1149-1154, 2018.

W. Luo, S. Pflugmacher, T. Pröschold, N. Walz, and L. Krienitz, Genotype versus Phenotype Variability in Chlorella and Micractinium (Chlorophyta, Trebouxiophyceae), Protist, vol.157, pp.315-333, 2006.

T. Proschold and F. Leliaert, Systematics of the green algae: conflict of classic and modern approaches BT -Unravelling the algae: the past, present, and future of algal systematics, vol.75, pp.124-153, 2007.

D. H. Cho, Microalgal diversity fosters stable biomass productivity in open ponds treating wastewater, Scientific Reports, vol.7, pp.1-11, 2017.

E. Kim, Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life, Proceedings of the National Academy of Sciences, vol.108, pp.1496-1500, 2011.

M. C. Oliveira, High-throughput sequencing for algal systematics, European Journal of Phycology, vol.53, pp.256-272, 2018.

C. V. Seppey, Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling, Soil Biology and Biochemistry, vol.112, pp.68-76, 2017.

A. R. Sherwood, M. N. Dittbern, E. T. Johnston, and K. Y. Conklin, A metabarcoding comparison of windward and leeward airborne algal diversity across the Ko' olau mountain range on the island of O'ahu, Hawai'i 1, Journal of Phycology, vol.53, pp.437-445, 2017.

V. Vasselon, I. Domaizon, F. Rimet, M. Kahlert, and A. Bouchez, Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?, Freshwater Science, vol.36, pp.162-177, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606868

R. Logares, Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities, Environ. Microbiol, vol.16, pp.2659-2671, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01258219

M. C. Pernice, Large variability of bathypelagic microbial eukaryotic communities across the world's oceans, ISME J, vol.10, pp.945-958, 2016.

K. M. Eriksson, Community-level analysis of psbA gene sequences and irgarol tolerance in marine periphyton, Applied and Environmental Microbiology, vol.75, pp.897-906, 2009.

J. D. Hall, K. Fucikova, C. Lo, L. A. Lewis, and K. G. Karol, An assessment of proposed DNA barcodes in freshwater green algae, Cryptogamie Algologie, vol.31, pp.529-555, 2010.

V. R. Marcelino and H. Verbruggen, Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae, Scientific Reports, vol.6, pp.1-9, 2016.

G. W. Saunders and H. Kucera, An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae INTRODUCTION, Algologie, vol.31, pp.487-528, 2010.

A. R. Sherwood, K. Y. Conklin, and Z. J. Liddy, What's in the air? Preliminary analyses of Hawaiian airborne algae and land plant spores reveal a diverse and abundant flora, Phycologia, vol.53, pp.579-582, 2014.

I. M. Bradley, A. J. Pinto, and J. S. Guest, Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities, Applied and Environmental Microbiology, vol.82, pp.5878-5891, 2016.

R. R. Gutell, N. Larsen, and C. R. Woese, Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective, Microbiological Reviews, vol.58, pp.10-26, 1994.

A. Pei, Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes, PLoS One, vol.4, 2009.

G. G. Presting, Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function, Canadian Journal of Botany, vol.84, pp.1434-1443, 2006.

A. R. Sherwood and G. G. Presting, Universal primers amplify a 23S rDNA plastid marker in eukaryotic algae and cyanobacteria, Journal of Phycology, vol.43, pp.605-608, 2007.

G. Lentendu, Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: A multiple barcoding approach, Molecular Ecology, vol.23, pp.3341-3355, 2014.

A. R. Sherwood, A. Kurihara, K. Y. Conklin, T. Sauvage, and G. G. Presting, The Hawaiian Rhodophyta Biodiversity Survey (2006-2010): a summary of principal findings, BMC Plant Biology, vol.10, 2010.

C. Berney, UniEuk: Time to Speak a Common Language in, Protistology! J. Eukaryot. Microbiol, vol.64, pp.407-411, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01512649

J. Del-campo, EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution, PLOS Biology, vol.16, 2018.

S. M. Adl, Revisions to the classification, nomenclature, and diversity of eukaryotes, J. Eukaryot. Microbiol, vol.66, pp.4-119, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02167105

M. Balvo?i?t?, D. H. Huson, . Silva, . Rdp, . Greengenes et al., BMC Genomics, vol.18, 2017.

C. Quast, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, pp.590-596, 2013.

L. Guillou, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucleic Acids Research, vol.41, pp.597-604, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01253994

J. Decelle, PhytoREF: A reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy, Molecular Ecology Resources, vol.15, pp.1435-1445, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01149047

F. Rimet, diatom: an open-access and curated barcode database for diatoms and freshwater monitoring, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01426772

S. Mordret, dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene, Molecular Ecology Resources, vol.18, pp.974-987, 2018.

M. V. Rossetto and H. Verbruggen, Reference datasets of tufA and UPA markers to identify algae in metabarcoding surveys, Data in Brief, vol.11, pp.273-276, 2017.

T. H. Yoon, Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community, PeerJ, vol.4, 2016.

S. Groendahl, M. Kahlert, and P. Fink, The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods, PLoS ONE, vol.12, pp.1-15, 2017.

S. Zou, How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae), Scientific Reports, vol.6, 2016.

P. Yilmaz, R. Kottmann, E. Pruesse, C. Quast, and F. O. Glöckner, Analysis of 23S rRNA genes in metagenomes -A case study from the Global Ocean Sampling Expedition, Systematic and Applied Microbiology, vol.34, pp.462-469, 2011.

S. M. Adl, The revised classification of eukaryotes, Journal of Eukaryotic Microbiology, vol.59, pp.429-493, 2012.
URL : https://hal.archives-ouvertes.fr/mnhn-02498504

M. D. Guiry, G. M. Guiry, and . Algaebase, World-wide electronic publication, 2018.

R. I. Jones, Mixotrophy in planktonic protists: an overview, Freshwater Biology, vol.45, pp.219-226, 2000.

B. C. Parker, Facultative Heterotrophy in Certain Soil Algae from the Ecological Viewpoint, Ecology, vol.42, pp.381-386, 1961.

T. Starks, L. Shubert, and F. Trainor, Ecology of soil algae: a review, Phycologia, vol.20, pp.65-80, 1981.

K. G. Porter, Phagotrophic phytoflagellates in microbial food webs, Hydrobiologia, vol.159, pp.89-97, 1988.

R. Rippka, Photoheterotrophy and chemoheterotrophy among unicellular blue-green algae, Archiv Für Mikrobiologie, vol.87, pp.93-98, 1972.

J. Kvíderová, C. E. Souquieres, and J. Elster, Ecophysiology of photosynthesis of Vaucheria sp. mats in a Svalbard tidal flat, Polar Science, 2018.

S. C. Agrawal, Factors affecting spore germination in algae -review, Folia Microbiologica, vol.54, pp.273-302, 2009.

L. M. Shields and L. W. Durrell, Algae in relation to soil fertility, The Botanical Review, vol.30, pp.92-128, 1964.

T. L. Starks and L. E. Shubert, Colonization and Succession of Algae and Soil-Algal Interactions Associated With Disturbed Areas, Journal of Phycology, vol.18, pp.99-107, 1982.

J. J. Cannone, The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs, BMC Bioinformatics, vol.3, 2002.

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Molecular Biology and Evolution, vol.33, pp.1870-1874, 2016.

J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.17, pp.368-376, 1981.

E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, vol.29, pp.2933-2935, 2013.

J. Sauze, The interaction of soil phototrophs and fungi with pH and their impact on soil CO 2 , CO 18 O and OCS exchange, Soil Biology and Biochemistry, vol.115, pp.371-382, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608085

S. Terrat, Mapping and predictive variations of soil bacterial richness across France, PLoS One, vol.12, pp.5-8, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01843156

S. Terrat, Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure, Microbial. Biotechnology, vol.5, pp.135-176, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01546177

S. Terrat, Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition, Microbial Biotechnology, vol.8, pp.131-142, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01215318

B. Kim, Deciphering Diversity Indices for a Better Understanding of Microbial Communities, J. Microbiol. Biotechnol, vol.27, pp.2089-2093, 2017.