title: Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii.
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 some 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 was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.
authors: Jornada Experimental Range, Agricultural Research Service, United States Department of Agriculture, Las Cruces, New Mexico, United States of America. malucero@nmsu.edu
authors: Mary E
authors: ME
authors: Lucero
authors: Adrian
authors: A
authors: Unc
authors: Peter
authors: P
authors: Cooke
authors: Scot
authors: S
authors: Dowd
authors: Shulei
authors: S
authors: Sun
mesh_terms: D027466:Atriplex / Q000166:cytology / Q000254:growth & development* / Q000382:microbiology* / Q000648:ultrastructure; D001419:Bacteria / Q000254:growth & development* / Q000302:isolation & purification; D001483:Base Sequence; D001499:Bayes Theorem; D044822:Biodiversity; D021901:DNA, Intergenic / Q000235:genetics; D005658:Fungi / Q000166:cytology / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification; D018525:Germination; D054892:Metagenome; D008969:Molecular Sequence Data; D012038:Regeneration / Q000502:physiology; D012639:Seeds / Q000166:cytology / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D021901:DNA, Intergenic