Abstract
Endophytic bacteria are nearly ubiquitously present in the internal tissues of plants, and some endophytes can promote plant growth. In this study, we sampled the roots of four ancestral species of sugarcane (two genotypes per species) and two sugarcane cultivars, and used 16S rRNA and nifH gene sequencing to characterize the root endophytic bacterial communities and diazotroph diversity. A total of 7,198 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. The endophytic bacterial communities exhibited significantly different α- and β-diversities. From the 202 detected families in the sugarcane roots, a core microbiome containing 13 families was identified. The nifH gene was successfully detected in 9 of 30 samples from the four sugarcane species assayed, and 1,734 OTUs were merged for endophytic diazotrophs. In the tested samples, 43 families of endophytic diazotrophs were detected, and six families showed differences across samples. Among the 20 most abundant detected genera, 10 have been reported to be involved in nitrogen fixation in sugarcane. These findings demonstrate the diversity of the microbial communities in different sugarcane germplasms and shed light on the mechanism of biological nitrogen fixation in sugarcane.
Highlights
Most crop plants grow in close association with microbial communities, which can be divided into three groups, endophytic, epiphytic, or closely associated
A total of 30 root samples were collected from 10 sugarcane varieties, including S. officinarum (Badila and Black Cheribon), S. robustum (51NG208 and FJDY), S. barberi (HATUNI and Katha), and S. spontaneum (HN-83 and FJ88-1), along with two commercial sugarcane cultivars (ROC22 and YT93-159)
Genomic DNA was successfully extracted, and the V3 and V4 regions of the 16S rRNA gene were amplified by polymerase chain reaction (PCR) using primers 341F and 806R
Summary
Most crop plants grow in close association with microbial communities, which can be divided into three groups, endophytic, epiphytic, or closely associated. Manipulation of the nitrogen fixation capacity of the sugarcane-associated microbiome has emerged as an alternative to nitrogen fertilizer application and has been extensively studied, especially for endophytic diazotrophs (Elbeltagy et al, 2001; Reis et al, 2004; Lin et al, 2014; De Souza et al, 2016; Proença et al, 2017). Many endophytic diazotrophs have been isolated and identified by culture-dependent methods, such as Gluconacetobacter diazotrophicus, Herbaspirillum rubrisubalbicans, Herbaspirillum seropedicae, Klebsiella spp. With the development of next-generation sequencing technologies, culture-independent methods have been employed to determine the profiles of the sugarcane-associated microbial communities by 16S rRNA sequencing (De Souza et al, 2016; Yeoh et al, 2016). There has been a focus on sequencing and identifying the nifH gene to isolate and characterize the diazotrophic community (Rouws et al, 2014; Li et al, 2017)
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