Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce ( Picea mariana ) Seedlings Grown in a Nursery

Abstract

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphereassociated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

“…In accordance with previous studies, we also observed shifts in the structure of bacterial community in diseased plants, but there were large differences in the extent of these changes. Similar to the results of this study, Filion et al (2004) have reported negative effects of root rot disease on the stability of the rhizosphere bacterial community of black spruce (Picea mariana) seedlings. In contrast, few studies have reported increase in bacterial diversity in pathogen-infested plants (Yang et al, 2001;Reiter et al, 2002).…”

“…In contrast, few studies have reported increase in bacterial diversity in pathogen-infested plants (Yang et al, 2001;Reiter et al, 2002). Interestingly, shifts in the structure of fungal community in response to pathogen infection have also been observed (Filion et al, 2004;Vujanovic et al, 2007). We postulate that the nature of fluctuations in the structure and function of plant-associated microbial community would be differentially determined by the virulence mechanism(s) of the pathogen and the response of host plant-to-pathogen infection.…”

“…Only few studies have examined the influence of phytopathogens on the microbial diversity of plant-associated bacterial community (McSpadden Gardener and Weller, 2001;Yang et al, 2001;Araujo et al, 2002;Reiter et al, 2002;Filion et al, 2004;Trivedi et al, 2010Trivedi et al, , 2011. To the best of our knowledge, ours is the first study to comprehensively report the changes in the functional diversity of plant-associated bacteria in response to pathogen infection.…”

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

“…Selection for Proteobacteria in the rhizosphere of Trifolium repens and Lolium perenne has been attributed to the nutrient-rich conditions of the rhizosphere (31), and similar results have been obtained in other plant systems, such as maize (38), soybean (52), and grasslands (42). However, in other woody species, such as chestnut trees (28) and black spruce (13), Acidobacteria have been shown to dominate rhizosphere systems. In our study, Proteobacteria were only slightly more prevalent (43% of sequences) than the Acidobacteria (38%), which may indicate a level intermediate between the copiotrophic and oligotrophic conditions thought to characterize the preferred habitats of these groups.…”

Culture-Dependent and Independent Analyses of the Microbial Communities Inhabiting the Giant Duckweed (Spirodela polyrrhiza) Rhizoplane and Isolation of a Variety of Rarely Cultivated Organisms within the Phylum Verrucomicrobia

“…Many studies on the microbial community structure of the rhizosphere and rhizoplane of terrestrial plants have been conducted using cultivation-based and cultivation-independent methods (12,18,21,22,31,40). These studies have shown that terrestrial plants harbor unique and diverse microbial communities in their rhizoplane probably due to the specific environments formed by the surface structure and exudates released from the roots.…”