Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions

Abstract

Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.

Trait-Based Comparison of Coral and Sponge Microbiomes

“…Many microbes produce siderophore compounds that chelate iron and are then taken up by the microbe. Siderophore production is a common feature of symbionts, including those of plants 97 , where it can facilitate iron acquisition and growth of the host 98,99 . Conversely, this trait is also common in pathogens, in which siderophores are used to sequester iron from the host or other organism 100 .…”

Insights into Streptomyces spp. isolated from the rhizospheric soil of Panax notoginseng: isolation, antimicrobial activity and biosynthetic potential for polyketides and non-ribosomal peptides

“…In this environment, they are exposed to a permanent state of competition; the production of specific antibiotics may play a decisive role in helping them survive within the rhizosphere microbial community [2]. Among them, it has been revealed that streptomycetes could help to promote the growth of host plants as well as to improve disease symptoms caused by plant pathogens through diverse mechanisms, including the production of bioactive metabolites, which are applied in the direct antagonism against pests and diseases [3,4], in the changes of host physiological function [5], in the induction of host systemic acquired resistances [6], and so on. Among these characteristics, a significant common function for Streptomyces is the antibiotics production [7], which suggests that streptomycetes play a key role in the plant defense and are widely recognized for their potentials in the biocontrol [2].…”

Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential

“…Reactive oxygen species (ROS) created by the plant cells, are generally neutralized by the production of enzymes such as superoxide dismutases (SOD), catalases (CatA), peroxidases (POD), alkyl hydroperoxide reductases (AhpC), genes conferring nitrosative stress caused by reactive nitrogen species, and glutathione-S-transferases (GSTs) in endophytes ( Khare et al, 2018 ). GST was found in the genome of Streptomyces scabrisporus NF3, an endophyte of Amphipterygium adstringens ( Ceapã et al, 2018 ). The ability to alleviate oxidative stress is one attractive property of plant growth promoting bacteria.…”