Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2011
Publication Date: 3/17/2011
Publication URL: http://handle.nal.usda.gov/10113/57951
Citation: Lucero, M.E., Unc, A., Cooke, P., Dowd, S., Sun, S. 2011. Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii. PLoS One. 6(3):e17693. Interpretive Summary: Microbial diversity was evaluated in two micropropagated saltbush species. Distinct and complex microbial communities were associated in vitro with each plant species. Fungal and bacterial cells were associated with epidermal layers of roots and shoots. Microbial cells were also found in vascular tissues and stomata. High throughput sequencing analysis revealed multiple species of fungi and bacteria, while small changes in primers used for amplification profoundly altered the abundance of individual taxa. The diversity of microbial communities associated with plants in vitro indicates the presence of multiple genomes poised to influence and interacts with whole plant physiology.
Technical Abstract: Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated those seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis is facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.