Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria

Abstract

BackgroundPlant endophytic bacteria play an important role benefiting plant growth or being pathogenic to plants or organisms that consume those plants. Multiple species of bacteria have been found co-inhabiting plants, both cultivated and wild, with viruses and fungi. For these reasons, a general understanding of plant endophytic microbial communities and their diversity is necessary. A key issue is how the distributions of these bacteria vary with location, with plant species, with individual plants and with plant growing season.ResultsFive common plant species were collected monthly for four months in the summer of 2010, with replicates from four different sampling sites in the Tallgrass Prairie Preserve in Osage County, Oklahoma, USA. Metagenomic DNA was extracted from ground, washed plant leaf samples, and fragments of the bacterial 16S rDNA genes were amplified for analysis of terminal restriction fragment length polymorphism (T-RFLP). We performed mono-digestion T-RFLP with restriction endonuclease DdeI, to reveal the structures of leaf endophytic bacterial communities, to identify the differences between plant-associated bacterial communities in different plant species or environments, and to explore factors affecting the bacterial distribution. We tested the impacts of three major factors on the leaf endophytic bacterial communities, including host plant species, sampling dates and sampling locations.ConclusionsResults indicated that all of the three factors were significantly related (α = 0.05) to the distribution of leaf endophytic bacteria, with host species being the most important, followed by sampling dates and sampling locations.

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.…”

The impact of zinc oxide nanoparticles on the bacterial microbiome of activated sludge systems

“…These microorganisms mainly include bacteria, protozoa, fungi and algae, which are actively involved in the process of removing nutrients and toxic materials from wastewaters123. Attempts to explain the mechanisms of the nutrient removal process have been focused mainly on dominant bacteria such as nitrifying bacteria, denitrifying bacteria and polyphosphate-accumulating organisms456.…”

Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants

“…(Reva et al 2002); Kocuria rhizophila was isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) (Kovács et al 1999); and Nocardiopsis dassonvillei was recovered as an agent to cause cutaneous and pulmonary infections (Brocq-Rousseau 1904); therefore, our study also improved the knowledge about the distribution of these bacteria. The host plant species has been reported as a major determinant for the endophytic bacterial communities (Ding et al 2013), as well as for the relative abundances of specific endophytic bacteria in the microbial community (Ding and Melcher 2016). In addition, the community structure and function of endophytic microbes are also related to environmental factors (Hartman et al 2008, Bannert et al 2011, Peralta et al 2013, including the soil metal contamination (Azarbad et al 2013).…”