## 1 Introduction  
Plants and microorganisms form complex associations displaying diverse interactions ranging from mutualism to pathogenicity. The habitat for microorganisms can be both the interior (endosphere occupied by endophytes) and the surroundings (phyllosphere, rhizplane, and rhizosphere occupied by epiphytes) of the host plant [1,2]. Microbial genomes, referred to as the microbiome or plants' second genome [2,3], constitute a specific plant microbiome together with the plant genome. Additionally, given the co-evolution process between plants and their associated microbiome resulting in a strong genomic interdependency, plants and their microbiome are considered as a metaorganism or a holobiont [4]. Plant-associated microbes, especially endophytes, play a crucial role in plant growth and development, allowing them to survive harsh conditions [1], which is important for food production (increased crops, biocontrol of plant diseases) and for coping with contaminants (phytrommediation). These beneficial microorganisms are termed as Plant Growth-Promoting Bacteria (PGPB) [3,5]. Their beneficial function is the improvement of plant fitness and protection against biotic and abiotic stresses by facilitation of nutrient acquisition and providing plant hormones and other metabolites [3; 6]. The presence of pollutants, such as heavy metals, may also pose a threat to both plants and some microorganisms (e.g., metal-tolerant species); however, they may be able to immobilize or decompose pollutants, thus protecting plants or improving their defense mechanisms. This issue is crucial for bioremediation and phytoremediation processes [7; 8]. Despite the enormous microbial abundance in different environments and the substantial progress in their cultivation methods, still only 1% of these microorganisms can be cultured [9]. In addition, some endophytes are commensals with a yet unknown function in plants. It is also very common to study the function of the microbiome for a specific group of species and to focus mostly on terrestrial plants rather than on a broader taxonomical spectrum of plant species [3]. Therefore, it is worth discovering microbiomes associated with plants providing new microbiomes that can potentially be valuable to humans. Valuable plants in terms of potential microbiome hosts are ferns belonging to the genus _Azolla_, which play important roles in some branches of industry [10; 11]. _Azolla filiculoides_ L. (_Salviniaceae_) is a small (2.5 cm) heterozygous floating aquatic or semiaquatic pteridophyte occurring on the surface of eutrophic waters in temperate and tropical climate around the world (Figure 1a). It can exist either individually or in mats, which can reach a thickness of up to 20 cm. The fern has bilobed leaves. The dorsal lobe has an ovoid cavity inhabited by the community of cyanobacteria _Anabaena azoliae_ (Starsb.) (Figure 1b) capable of atmospheric nitrogen fixing using the nitrogenase enzyme (EC 1.18.6.1) in specialized thick-walled cells called herocystis (Figure 1c). Figure 1: (**a**) Culture of _A. filiculoides_ under laboratory conditions on IRRI medium; (**b**) filaments of _A. azoliae_ in a leaf cavity; (**c**) close up of _A. azoliae_; both pictures taken from the light microscope at magnifications of 10x and 100x, respectively (Nikon Eclipse 80i, Nikon Instruments Europe B.V., Amsterdam, The Netherlands). Photo: [PERSON]. This trait makes _Azolla_ sp. independent of other external nitrogen sources allowing its fast growth and production of high-protein biomass. Hence, _Azolla_ sp. can be used as a green manure on rice fields and animal feed [10; 11]. Another important feature of the fern is its capability of heavy metal accumulation [11; 12]. Over the years, the cyanobiont has been named _Nostoc azollae_, _Anabaena azollae_, and _Trichormus azollae_, but no definitive classification exists to date. Studies by [PERSON] et al. [13] suggested that the endosymbiont represents rather _Nostoc_ sp. than _A. azollae_.