We have dislodged epiphytes using methods similar to those reported by others [13, 26–28]. Since we did not test the rinse water for rDNA amplicons, we cannot be sure that we have removed all epiphytic bacteria. However, the observation that the complexities of the populations (Additional file 1: Table S5) were substantially lower than those reported for leaf epiphytic bacteria [29, 30] suggests that most epiphytes have been removed. Past studies have applied multiple enzyme digestion T-RFLP to environmental
bacterial community research [31–33]. Some studies have focused on the rhizosphere, selleck chemicals llc rhizoplane and the epiphytic phyllosphere bacterial communities using fingerprint techniques of 16S rRNA genes, especially the rhizosphere of single cultivated plant species including potato and rice [34–36] and the phyllosphere of soybean, rice and maize [6, 37]. The present research is the first to apply single digestion T-RFLP to leaf endophytic bacteria in multiple host species. Multi-enzyme studies depend on a reliable T-RFLP database to deduce species information; however
most T-RFLP databases are still developing, so that a large proportion of novel bacteria, which are highly abundant in the environment, may not be matched using current databases . Although closely related bacterial species will usually produce the same T-RF, one or more other distinct taxonomic groups may also produce the same T-RF. Therefore variation in abundance of a T-RF may be due to changes in one AMN-107 clinical trial of the represented taxonomic groups, while a second is unchanged. Multi-enzymes are used in an effort to make taxonomic assignments; however taxonomic assignments are not necessary for identification of the factorial influences on the leaf endophytic bacterial communities, as studied in this work. Single digestion T-RFLP peaks represent OTUs (Operational T-RFLP Unit) that provide information on the diversity of leaf endophytic bacteria in different environments. also In order to assess the abilities
of T-RF OTUs present in individual plants to compete with other bacteria, we focused on the relative amounts of T-RF OTUs in different plants only in those plants in which they were found. The APE of a T-RF in one host species was defined as the average proportion of a T-RF in all the LY3023414 mw samples of one plant species which have this T-RF. Calculating APE rather than regular average proportion can avoid the problem of underestimation of the abundance of a T-RF in one host species due to non-infection of the bacterial species represented in some samples. The APE of a T-RF can more accurately reflect the overall compositions of leaf endophytic bacterial communities in a plant species than can methods that include absence in the analysis.