Microbes such as fungi and bacteria can exist within seed as endophytes, which have been associated with increasing seed germination and plant root development but can also be latent plant pathogens and some can cause seed decay. Current research is focussed on agricultural plants, with knowledge of the diversity in natural ecosystems lacking, limiting their application to restoration and ex situ conservation. We studied the taxonomic and functional diversity of seed microbiomes of one native Australian tree (Melaleuca quinquenervia) and two native grasses (Microlaena stipoides and Themeda triandra), which are used in ecosystem restoration projects. We sampled from fifty-two sites in NSW and the ACT. We identified fungi and bacteria from metabarcoding of the internal transcribed spacer region ITS2 of the rRNA (fungi) and the V4 region of the 16S rRNA gene (bacteria). It is important to identify key members of the seed microbial community, which could mitigate the low rates of germination and establishment characteristics of many plant species in restored sites, especially grassland ecosystems. Our results uncovered a diverse seed microbiome representing two fungal phyla (223 families) and 20 different bacterial phyla (159 bacterial families), from all the host species combined. Melaleuca quinquenervia was dominated by the bacteria Sphingomonas and Sediminbacterium, and the fungi Pestalotiopsis and Neophaeomoniella. Microlaena stipoides and T. triandra shared a similar microbiome, dominated by the bacteria Pantoea and Pseudomonas, and the fungi Alternaria and Cladosporium.
We also have a microbial pure culture collection isolated from the seed (450 bacterial cultures and 520 fungal cultures) and are phenotyping them for plant growth promotion traits (auxin production, the ability to produce siderophores and 1-aminocyclopropane-1-carboxylic acid deaminase) and nitrogen fixation ability, to provide insight into their potential role in plant fitness and for improving restoration efforts for these plant species.