Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis

Abstract

The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f-1492r) was selected to specifically amplify bacterial 16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs (Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in rice roots.

Diversity of bacterial endophytes in roots of Mexican husk tomato plants (Physalis ixocarpa) and their detection in the rhizosphere

“…In this study, we analyzed the endophytic bacterial diversity of husk tomato roots. Our results suggest that the most dominant group was affiliated with Gammaproteobacteria, which is consistent with other studies (Chelius and Triplett, 2001;Kaiser et al, 2001;Sun et al, 2008). This class included 7 of 16 OTUs found in the library, which means more than 50%.…”

“…Forty-one clones showed high identity with the Stenotrophomonas sp and S. malthophilia species. Stenotrophomonas species have been isolated or detected as endophytes from rice roots (Sun et al, 2008), dune grasses (Dalton et al, 2004) and cotton roots and stems (McInroy and Kloepper, 1995). Some studies have reported species of Stenotrophomonas as a plant growth-promoting bacterium that can suppress disease development by secretion of some compounds, such as the antibiotic maltophilin (Jakobi et al, 1996).…”

Biodiversity and biotechnological applications of halophilic microbes for sustainable agriculture

“…There are very few reports of archaea as associated with plants such as maize, rice, and halophytic plant (Abutilon, Cressa, Sporobolus, and Suaeda nudiflora) [17][18][19]. Archaea have been reported as unculturable from maize [20] and rice crop [21], whereas culturable archaea have been reported from Abutilon, Cressa, Sporobolus, S. nudiflora [22] [17,23,24]. Microbiome of saline environments, especially halophilic fungi, has become one of the richest bioresources for industrially important molecules and enzymes.…”

Functional Genes of Microorganisms, Comprehending the Dynamics of Agricultural Ecosystems

“…For example, the PCR-DGGE technique, besides from inferring communities that are present in soil and water, may also help to identify epiphytic 6 and endophytic bacterial communities 7,8 , which are relevant in agroecosystems studies. Agroecosystems provide different environments with a wide variety of microhabitats.…”