Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing

Abstract

As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ) to 96.08% (YN), and Delftia (10.39–38.42%), Burkholderia (2.71–15.98%), Escherichia/Shigella (4.90–25.12%), Pseudomonas (2.68–30.72%) and Sphingomonas (1.83–2.05%) dominated in four planting bases. Pseudomonas (17.94–22.06%), Escherichia/Shigella (6.59–11.59%), Delftia (9.65–22.14%) and Burkholderia (3.12–11.05%) dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples.

Butyrate Protects Mice Against Methionine–Choline-Deficient Diet-Induced Non-alcoholic Steatohepatitis by Improving Gut Barrier Function, Attenuating Inflammation and Reducing Endotoxin Levels

“…The genus Coprobacillus and another butyrate-producing genus, Coprococcus , have been found to play beneficial roles in maintaining intestinal stability ( Arrazuria et al, 2016 ; Mancabelli et al, 2017 ; Nishino et al, 2017 ; Walsh et al, 2017 ). The probiotic properties of Delftia are due to the ability of this genus to transform or degrade multiple organic and inorganic toxins ( Li et al, 2017 ). Furthermore, Sutterella , an organism that promotes a protective immunoregulatory profile in vitro ( Berer et al, 2017 ), and Coriobacteriaceae , some species of which have been suggested to improve host lipid metabolism ( Raza et al, 2017 ), were also increased following butyrate treatment.…”

Changes in Acetylene Reduction Activities and nifH Genes Associated with Field-Grown Sweet Potatoes with Different Nursery Farmers and Cultivars

“…Regarding the specificity of the universal primer set for nifH [13] used in this study, the results in the other reports using this primer set for analyzing diversity of nifH in sweet potatoes [16], an epiphyte orchid, Dendrobium catenatum Lindl. [17], and Himalayan soils [18] suggested that there seemed to be no apparently biased PCR amplification by the primer set. Table 4.…”

Rizobacterias promotoras de crecimiento en Guarianthe skinneri (Orchidaceae)

“…En aquellas bacterias que tienen la capacidad de romper este enlace, serán detectados por el cromatógrafo de gases los picos correspondientes a cada compuesto, evidenciando así la participación de la enzima en la reducción de acetileno a etileno. Diversas bacterias presentes en las raíces de las orquídeas se han caracterizado mediante la detección del gen nifH que codifica para la enzima nitrogenasa en la fijación del nitrógeno (Álvarez-López et al, 2014;Yang et al, 2014;Li et al, 2017).…”

“…Estas bacterias hacen disponible el N atmosférico para las plantas y son consideradas como BPCV por presentar funciones que favorecen la disponibilidad de nutrientes (Glick, 2012). Li et al, (2017) mencionan que las bacterias diazotrófas se encuentran presentes en la mayor parte de los tejidos aportando nitrógeno, a pesar que también se encuentran otros géneros bacterianos cumpliendo en las raíces. En ocasiones las bacterias no presentan interacciones beneficiosas con plantas debido a que las bacterias fijadoras de N 2 que no forman simbiosis no son tan efectivas como las bacterias simbióticas (Álvarez-López et al, 2014).…”

“…Se han aislado bacterias benéficas a partir de las raíces de diversas orquídeas, muchas de estas presentan la capacidad de producir ácido indolacético (AIA) como Burkholderia sp., Bacillus sp., Pseudomonas sp., y Agrobacterium sp., (Tsavkelova, Cherdyntseva, Botina, & Netrusov, 2007a), Bacillus sp., Burkholderia sp., Enterobacter sp., y Curtobacterium sp., (Galdiano-Júnior, Pedrinho, Castellane, & Lemos, 2011), Paenibacillus sp., (Faria, Dias, Melo, & Carvalho-Costa, 2013). Al igual bacterias fijadoras de nitrógeno (Zambrano-Ramos, Salgado-Jiménez, & Hernández-Tapia, 2007;Álvarez-López, Osorio-Vega, Díez-Gómez, & Martín-Montoya, 2014;Yang et al, 2014;Villegas-Espinoza et al, 2014;Li et al, 2017). Se han reportado otras bacterias solubilizadoras de fosfato inorgánico como Serratia sp.…”