Specialized bacteriome uncovered in the coralloid roots of the epiphytic gymnosperm, Zamia pseudoparasitica

Abstract

Epiphytes face several constraints regarding nutrient acquisition: They are disconnected from soil minerals and they have to mainly rely on nutrients leached by precipitation and microbes. The cycad, Zamia pseudoparasitica Yates, is the only known strictly epiphytic gymnosperm, and it is endemic to Panamanian rainforests. Cycads have evolved specialized coralloid roots that host endophytic cyanobacteria specialized in nitrogen fixation. We collected coralloid roots from plants in the Omar Torrijos National Park, Provincia de Coclé. DNA was extracted from fresh inner coralloid roots, and the bacteriome was described using two molecular markers: rbcL-rbcX (targeting cyanobacteria) and 16S (all bacteria). Sixteen samples were sequenced for rbcL-rbcX yielding sequences belonging to a monophyletic group within the order Nostocales. One hundred and sixty-five amplicon sequence variants (ASVs) were found in at least two of our 27 samples amplified for 16S. Nostocales, Rhizobiales, and Acetobacterales were the three most diverse and abundant orders of bacteria found within the coralloid roots, and the candidate phylum WPS-2 was also found in many samples. We performed a de novo assembly from a single culture of the endophytic cyanobacteria. A phylogenomic analysis of the isolate places the cyanobacterium in a sister clade to mostly symbiotic taxa from mosses, liverworts, and lichens. Additionally, the isolate has genes putatively involved in symbiotic signaling, hormogonium differentiation, ammonium transport, nitrogen fixation, heterocyst differentiation, sulfate transport, and secondary metabolites. Although dominated by organisms with the capacity to fix nitrogen, coralloid roots are also inhabited by a diverse community of other taxa which may also play biologically important roles.