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.

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

“…This indicates that the DNA extraction procedure introduces significant bias, thereby influencing the interpretation of the microbial community observed. PCR-based metagenomic approaches such as DGGE Ramond et al, 2013), t-RFLP (Sessitsch et al, 2012;Ding et al, 2013) and next generation sequencing (Gottel et al, 2011;Lucero et al, 2011;Ìnceoğlu et al, 2011;Molina et al, 2012) are continuously used to elucidate the structure and ecological roles of plant-associated (and other) microbial communities. However, few, if any, of these studies share the same DNA extraction protocol and/or are preceded by an evaluation of DNA extraction procedures to select the most efficient.…”

Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches

“…Several previous studies reported the occurrence of those species in other plants, including banana (Cao et al, 2002), Aegle marmelos (Gond et al, 2007), Coffea Arabica L. (Fernandes et al, 2009), tangerine andlemons (Dini-Andreote et al, 2009), Deschampsia antarctica Desv. (Rosa et al, 2009), Huperzia serrata (Wang et al, 2011), Bletilla ochracea (Tao et al, 2008), wheat (Smit et al, 1999), Atriplex canescens (Lucero et al, 2011), and Artemisia species (Huang et al, 2009). The group of Pleosporaceae represented by Alternaria species consists mainly of saprophytes that are commonly found in soil or on decaying plant tissues; however, some of them were reported to acquire pathogenic traits (Thomma, 2003).…”

“…Although commonly cultivable, this genus was only detected in this study by clone sequencing and appropriate media should be optimized to isolate and culture this genus in date palm. Cladosporium species are commonly found in many other plants (both herbaceous and woody) and in soil (Arx, 1949;Fisher et al, 1995;Taylor et al, 1999;Bensch et al, 2010), including wheat (Smit et al, 1999), pharmaceutical plants (Heterosmilax japonica) (Gao et al, 2005), and Atriplex canescens (Lucero et al, 2011) where they constitute an extremely large and important genus of plant pathogens. However, Cladosporium also includes cosmopolitan and ubiquitous saprotrophs.…”

Exploring interactions of plant microbiomes

“…A comparative analysis between the endophytic microbial communities of Atriplex canescens and A. torreyi, two halophilic plants used as forage in North America, revealed the presence of distinct communities between the two species, mostly differing in the prevalence of diazotrophic bacteria (Lucero et al, 2011). That finding was directly related to the metabolic differences observed between the two plant genotypes, which can also account for changes observed in plants from distinct genotypes within the same species (i.e., varieties, cultivars).…”