Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora

Abstract

Understanding plant-microbe interactions with the possibility to modulate the plant’s microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.

Six novel Micromonospora species associated with the phyllosphere and roots of leguminous plants: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov., and Micromonospora trifolii sp. nov.

“…, shows the distribution of carbohydrate binding module proteins (CBM), carbohydrate esterases (CE), glycoside hydrolases (GH), glycosyl transferases and polysaccharide lyases (PL) found for each genome. These results confirm the importance of carbohydrate metabolism in Micromonospora strains associated to endophytic habitats [27]. As an example, beta -glucosidases involved in the hydrolysis for cellulose were found in as many as six copies.…”

“…Genome sequencing, assembly and annotation were performed as described before [12]. The genome size of the new Micromonospora strains varied from 6.8 (strain PSH25 T ) to 7.6 Mb (strain MED01 T ), values which are in the range of average Micromonospora genomes, as reported previously [27]. The number of coding DNA regions (CDS) was 6243 (strain LAH09 T ) to 7050 (strain MED01 T ).…”

“…It has been reported that micromonosporae isolated from plant material are characterized by their capacity to produce plant growth promoting factors such as siderophores, metallophores, phytohormones and others [27,42,45]. The new isolates and their taxonomic neighbours were also screened for the presence of genes related to these features.…”

Integration of Omics Approaches Enhances the Impact of Scientific Research in Environmental Applications

“…Thus, it is crucial to work in multidisciplinary teams, where one of the key people is a specialist from the bioinformatics field [ 54 ]. Experience in information technology (IT) programming and artificial intelligence (AI) pipeline development for integrative database construction is also necessary [ 55 ]. Working with such enormous amounts of data and finding new patterns among observed results requires both adequate tools and critical thinking in interpreting the findings [ 56 , 57 ].…”

In Vitro Screening of Endophytic Micromonospora Strains Associated with White Clover for Antimicrobial Activity against Phytopathogenic Fungi and Promotion of Plant Growth

“…Endophytic Micromonospora isolates, successfully recovered from different parts of various plants including the roots, leaves, or root nodules of legume and actinorhizal plants [11], have been shown to be beneficial for plants, with an important role as plant-growth-promoting 2 of 11 bacteria (PGPB) and biocontrol agents [6,12]. Many of them have been recovered and investigated in the last decade [13,14]. In this study, nineteen endophytic bacterial isolates originating from the root nodules of white clover were recovered and classified into the genus Micromonospora.…”