Tomato-Associated Archaea Show a Cultivar-Specific Rhizosphere Effect but an Unspecific Transmission by Seeds

Archaea have recently been identified as substantial members of the plant microbiome. As for other microorganisms, the rhizosphere is a favorable habitat for archaea; however, less is known about their community assembly, composition, or origin. Therefore, we analyzed archaeal communities in the rhizosphere of tomato plants (Solanum lycopersicum ‘Moneymaker’ and ‘Hildares F1’) nurtured in two different soil types. In complementary experiments, archaeal communities were assessed in two generations of tomato seeds. The abundance of the archaea was significantly different for each plant genotype and habitat. In the rhizosphere of Moneymaker, the archaeal abundance was 10-fold higher than in Hildares F1, whereas the decrease in archaeal abundance from seeds of the first generation to the second was much higher by 104-fold in the same cultivar. Overall, the archaeal community in tomato was dominated by Thaumarchaeota and Euryarchaeota. The core community in tomato consisted of species assigned to the Soil Crenarchaeotic Group (Thaumarchaeota; 60.7%), Methanosarcina (Euryarchaeota; 12.6%), Methanoculleus (Euryarchaeota; 3.4%), and unassigned archaeal species (7.2%). Differences in abundance, diversity, and composition between cultivars were so distinct that they masked any effect determined by the different composition of soil. In seeds, archaeal abundance and diversity was comparably low and the composition showed random patterns; no indications of a plant-mediated vertical transmission were found. We assume that archaea represent only bystander microorganisms in seeds, while their cultivar-specific enrichment in the rhizosphere suggests a role in functioning of the plant holobiont.