Supplementary Materials of "Unravelling the genomic and functional arsenal of Bacilli endophytes from plants with different lifestyles"
Arapitsas, Nikolaos; Christakis, Christos; Paragkamian, Savvas; Soultatos, Stefanos; Reden, Franziska; Psarologaki, Chrysianna; Avramakis, Emmanouil; Stamatakis, Alexandros; Markakis, Emmanouil; Sarris, Panagiotis
- Publisher
- Zenodo
- Language
- en
Abstract
The ongoing environmental crisis requires sustainable farming to ensure food security. Endophytes, and in particular endophytic species of the Bacilli class, exhibit promising agricultural potential by promoting plant growth, controlling challenging plant pathogens, and producing a substantial variety of secondary metabolites. Unraveling the phylogeny of this class in conjunction with genome mining and comparative genomics provides unique insights into the evolutionary relationships among its members and can reveal novel traits that will be crucial for future biotechnological and agrifood applications. We thoroughly study 25 novel endophytic Bacilli strains that we isolated from various halophytic plants and olive trees on Crete and Chrysi island. We evaluate the ability of these isolates to grow under increased salinity, to inhibit the growth of economically important phytopathogens in vitro, and enhance plant tolerance against biotic and abiotic stress. We employ a hybrid sequencing approach that combines Illumina short-reads and PacBio long-reads, to accurately reconstruct the complete genome of each isolate. Genome mining and comparative genomics analyses identify genes that are associated with plant-growth promotion, production of secondary metabolites as well as antimicrobial compounds, and an increased genetic novelty among the genomes of our isolates. Furthermore, we infer a well-supported phylogeny that includes our isolates as well as publicly available Bacilli representatives. We identified four putatively novel species and show that these isolates and even isolates of already well-studied species (e.g., Bacillus thuringiensis) may harbor yet unidentified protein-coding genes and secondary metabolites. Our study highlights the increased genetic, functional, and taxonomic novelty that reside within endophytic strains of a well-studied class and emphasizes the value of deep exploration of endophytic microbial genomes and communities for microbiology, ecology and agriculture.
Full text
Unravelling the genomic and functional arsenal of Bacilli endophytes from plants with different lifestyles Nikolaos P. Arapitsas1,2¶, Christos A. Christakis1,2¶, Savvas Paragkamian1¶, Stefanos Soultatos1,3, Franziska Reden1,4, Chrysianna Psarologaki1, Emmanouil Avramakis5, Alexandros Stamatakis4,6,7, Emmanouil A. Markakis3, Panagiotis F. Sarris1,2,8* Supplementary Figures Supplementary Figure S1 Whole-genome maps of the isolates SRL179, SRL337 and SRL543, representing putative new species, produced using the Bakta annotation pipeline.
Supplementary Figure S2 Bar plot for all in vitro tested fungal phytopathogens for the different batches and assays concerning the radial growth rate in mm. Supplementary Figure S3 Bar plot for all in vitro tested fungal phytopathogens for the different batches and assays concerning the number of conidia.
Supplementary Figure S4 Bar plot for Botrytis cinerea pathogen for the different batches and assays concerning the number of sclerotia.
Supplementary Figure S5 Inhibition of fungal growth of A. Alternaria sp., B. Botrytis cinerea and C. Fusarium oxysporum f.sp. radicis-cucumerinum by the most effective Bacillus isolate (SRL163) in dual-plate assays.
Supplementary Figure S6 Bar plot for all in vitro tested fungal phytopathogens for the different batches and assays concerning the hyphae width measured in μm. Supplementary Figure S7 Bar plot for all in vitro batches for Verticilium dahliae concerning the microsclerotial area measured in cm2.
Supplementary Figure S8 A. Number of isolate-specific orthogroups per isolate. B. Percentage of genes attributed to orthogroups across isolates. C. Number of orthogroups per isolate shared with all isolates (core orthogroups) (yellow, bottom bars) and orthogroups shared with at least one but not all isolates (partially shared orthogroups) (blue, top bars).
Supplementary Figure S9 UpSet plot of the pangenome analysis of the Bacillus thuringiensis isolate SRL368 and its five closest relatives, including the B. thuringiensis isolates SRL215, SRL218 and SRL224. Horizontal bars (left) represent the total gene clusters per genome, and vertical bars (top) display the number of shared clusters for each intersection (genome combination) indicated by the connected dots below.
Supplementary Figure S10 Distribution of BGC counts per isolate by similarity confidence. Each stacked bar plot shows the number of BGCs identified in each isolate. Colors indicate the similarity confidence of each BGC to known clusters based on the antiSMASH database: High, Medium, Low, and Undefined (no close matches). Supplementary Figure S11 Average number of BGCs per genus across the genomes of the 25 isolates. Bars showing mean antiSMASH region counts per genus ± standard error (SE). The value of n above each bar indicates the number of isolates, among the 25 analyzed, belonging to each genus.
Supplementary Figure S12 BGC classes content of each isolate. Pie charts showing the relative proportions of BGC classes identified in each of the 25 isolates. Different colors correspond to eight BGC categories: NI-siderophores, NRPS, NRPS-PKS hybrids, NRPSother hybrids, others, PKS, RiPPs and terpenes (see SM 1 - Supplementary Methods). For each isolate, percentages are calculated by dividing the number of BGCs of a given class by the total number of predicted BGCs in that isolate.
