Abstract
Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.
Highlights
Endophytic microorganisms, bacteria or fungi, are known to inhabit plant tissues without causing disease symptoms in the host plant (Hallmann et al 1997; Reissinger et al 2001; Wilson 1995)
The results showed that LK11 produces different quantities of GAs in its pure culture; these included G A1, GA3, GA8, GA9, GA24, GA53, GA12, GA20, GA19, GA34, GA4, and G A7 (Fig. 1a)
Physiologically active GA3 and GA4 were produced in significantly high quantities while inactive GA53 and G A19 were abundant in the pure culture of Sphingomonas sp
Summary
Endophytic microorganisms, bacteria or fungi, are known to inhabit plant tissues without causing disease symptoms in the host plant (Hallmann et al 1997; Reissinger et al 2001; Wilson 1995). Endophytic microbial communities have vital roles in the development and growth of various host plants under favorable and various stress conditions, such as heat, salinity, heavy metal contamination, and drought (Yaish et al 2015). Bacteria have a knack for inhabiting internal plant tissues and imparting beneficial effects for host growth. Such traits have been shown to improve growth and developmental processes (Glick 1995; Ryan et al 2008) of the host through the ability of endophytes to perform a range of functions, including assisting both primary and secondary nutrient uptake via atmospheric nitrogen fixation (Gothwal et al 2008), synthesizing iron siderophores (Wang et al 1993), and solubilizing minerals such as phosphate, potassium, and. There are few reports describing Sphingomonas species as endophytes
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