Halophytes as holobionts: disentangling the contribution of plant genotype and environmental factors to the associated microbiome of hydro- and xerohalophytes.

Halophytes are of great interest for their ecosystemic benefits and valuable secondary metabolites. However, they are threatened by factors such as heat waves, drought, increased salinity and pollution, associated with climate change and human activity. In this context, their associated microbial communities are crucial for their survival. Despite that, there are no comparative studies on microbial communities associated with two types of halophytes: hydrohalophytes (plants from humid saline environments) and xerohalophytes (plants from saline arid environments). This study aimed to investigate the factors that determine the structure of microbial communities of three hydrohalophytes of the Southwest Spain (Atlantic coastal), in particular Atriplex portulacoides, Salicornia perennis and Suaeda vera; and three xerohalophytes of Southeast Spain (Mediterranean coast and inland saltmarshes), namely, Atriplex glauca, Anabasis articulata and Halocnemum strobilaceum. Samples were collected in three locations and two seasons (autumn and spring) to analyze how plant genetics and environmental factors influence their microbiota. The analysis was done by sequencing the 16S V3-V4 region in samples of different plant compartments: endophytes, rhizosphere soils and bare soils. The results showed strong attraction of bacteria and archaea to the rhizosphere, although further tight selection limits the number of endophytes. A "core" of endophytes common to both functional halophytes was identified, including the genera Kushneria, Halomonas, Pseudoalteromonas and Zunongwangia, which were considered generalists. In addition, specific genera considered as specialists were found: hydrohalophytes showed affinity for Vibrio, Pseudomonas and Marinomonas, while xerohalophytes harbored Marinilactobacillus, Alkalicoccus, Alkalibacterium and Arthrobacter. Although most endophytes persist across seasons, their relative abundances can change for better adaptation. Clear differences were also encountered among the rhizosphere inhabitants in both functional halophytes: whereas halophilic ammonia oxidizing archaea were prevalent in the rhizosphere of hydrohalophytes, versatile adaptive bacteria were predominant in that of xerohalophytes. These microorganisms play vital roles, including promoting plant growth, participating in the carbon and nitrogen metabolisms, and recycling organic matter. In conclusion, the study determined that the main factors shaping the microbial populations associated to halophytes were: halophyte type > halophyte species > soil characteristics > seasonality.