Can plants live without roots and soil? The answer is "yes," and air plants, or epiphytic Tillandsias, are an interesting and vivid exemplar of surviving in aerial niches. These marvelous plants belong to the Bromeliaceae family and are renowned for their extraordinary capacities to survive without soil, evolving into specialized leaf trichomes that enable the absorptive functions typically served by roots (Fig. 1).

The evolution of air plants raises several intriguing questions: When and where did they make the shift from terrestrial to aerial habitats, and what drove this transition? What is the genetic basis for the loss of root function in air plants? How do the specialized trichomes on their leaves actually take over the absorption functions that roots typically perform? And most importantly, how do they acquire the essential nutrients in their aerial environments? 

In this study, we utilize multi-omics approaches to decipher the evolutionary tempo and dynamics of air plants, as well as to understand the genetic foundations of their distinctive adaptive traits and potential survival strategies regarding nutrient acquisition.

Origin of air plants

To trace the origins of air plants, we constructed a comprehensive phylogenetic tree of the Tillandsioideae subfamily using multiple nuclear genes from 147 newly sequenced transcriptomes. This tree captures 78% of the genera within the subfamily. Our ancestral reconstruction and evolutionary dynamics analysis indicate that core tillandsioids originated approximately 11.3 million years ago in the Andes. The significant geological uplift of the Andes facilitated the emergence of atmospheric tillandsioids, which are commonly known as air plants.

Genetic basis for root function loss and change in air Plants

Tillandsioids, particularly atmospheric varieties, exhibit poorly developed root systems that primarily function as mechanical holdfasts instead of canonical roots. Our analysis of key genes involved in root development revealed signs of positive selection or rapid evolution in these genes. Notably, the SCR and JKD loci, which are associated with root tissue development, displayed significant evolutionary changes. Comparisons between epiphytic tillandsioids and terrestrial bromeliads revealed distinct differences in the evolutionary trajectories of several genes, with SCR and WER undergoing stronger selection pressures in tillandsioids. Moreover, we observed that genes crucial for gravitropism and lateral root development, such as ARG1 and ANR1, have been lost or reduced in tillandsioids. These findings suggest the evolutionary adaptations that enhance the ability of air plants to thrive in atmospheric niches. Additionally, the roots of tillandsioids show significant lignification, which increases their mechanical strength as holdfasts. Spatial transcriptomic analysis further revealed distinct molecular characteristics and gene expression patterns associated with secondary cell wall (SCW) biogenesis in various cell types, confirming the crucial contributions of these deformed roots to mechanical supportive function.

Absorption functions of specialized leaf trichomes

As the roots lose their ability to absorb water and nutrients, specialized trichomes in the leaf epidermis of epiphytic bromeliads take on this role. These multicellular trichomes consist of a living stalk and a dead shield, characterized by a thin cuticle layer that prevents capillary flow, which is essential for their absorption capabilities. Functional enrichment analysis identified co-expanding gene families related to cuticle biosynthesis, including tandem repeats of the CYP96A15 gene in the T. duratii genome. In situ hybridization experiments demonstrated that these CYP96A15 duplicates are specifically expressed in the dome and foot cells of trichomes, underscoring their critical role in the absorption functions of these structures.

Nutrient acquisition in aerial environments

To understand how air plants forage essential nutrients in their aerial environments, we employed 16S rRNA sequencing and metagenomic approaches to conduct a comprehensive analysis of the phyllospheric microbial communities. Our findings revealed a significant abundance of nitrogen-fixing bacterial communities with host-specificities that co-evolved with the diversification of epiphytic tillandsioids. Notably, the bacterial genus 1174-901-12 appears to be a primary source of nitrogen for air plants, particularly in nutritionally deficient aerial environments.

In summary, our study presents a comprehensive analysis of the evolutionary dynamics and genetic signatures of the rapid differentiation, speciation, dispersal and adaptation to various habitats and aerial ecological niches in air plants (Fig. 2). This study illuminates the evolutionary trade-offs and adaptive evolution of air plants exposed to extreme climate fluctuations with geological uplift of Andes.