Ecology

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ReferencesMariani, M. et al. Front. Ecol. Environ. https://doi.org/10.1002/fee.2395 (2022).Article 

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Positive correlation between biosynthetic gene cluster (BGC) and phylogenetic distance in the genus Bacillus
BGCs are responsible for the synthesis of secondary metabolites involved in microbial interference competition. To investigate the relationship between BGC and phylogenetic distance within the genus Bacillus, we collected 4268 available Bacillus genomes covering 139 species from the NCBI database (Supplementary Data 1). Phylogenetic analysis based on the sequences of 120 ubiquitous single-copy proteins27 showed that the 139 species could be generally clustered into four clades (Fig. 1 and Supplementary Data 2; the phylogenetic tree including all the detailed species information is shown in Supplementary Fig. 1), including a subtilis clade that includes species from diverse niches and can be further divided into the subtilis and pumilus subclades, a cereus clade that contains typical pathogenic species (B. cereus, B. anthracis, B. thuringiensis, etc.), a megaterium clade, and a circulans clade.Fig. 1: Phylogram of the tested Bacillus genomes.The maximum likelihood (ML) phylogram of 4268 Bacillus genomes was based on the sequences of 120 ubiquitous single-copy proteins27. The phylogenetic tree shows that Bacillus species can be generally clustered into the subtilis (light green circle; further includes subtilis (dark green) and pumilus (blue) subclades as shown in the branches), cereus (red), megaterium (yellow), and circulans (gray) clades. For detailed information of the species, please refer to the phylogenetic tree in Supplementary Fig. 1.Full size imagePrediction using the bioinformatic tool antiSMASH15 detected 49,671 putative BGCs in the 4268 genomes, corresponding to an average of 11.6 BGCs per genome (Supplementary Data 3). The subtilis clade had the most BGCs, 13.1 BGCs per genome (Fig. 2a); the subtilis subclade especially accommodates a high abundance of BGCs as 13.6 per genome (Supplementary Fig. 2a), which corresponds to their adaptation in diverse competitive habitats such as plant rhizosphere. The cereus and megaterium clades possessed moderate number of BGCs as 11.7 and 7.4 per genome, respectively; while the circulans clade only had 4.3 BGCs/genome (Fig. 2a and Supplementary Table 1), suggesting a distinct physiological feature and niche adaptation strategy. The two most abundant BGC classes were nonribosomal peptide-synthetase (NRPS) and RiPPs, which had an abundance of 3.7 and 3.1 per genome on average, respectively (Supplementary Fig. 2b and Supplementary Table 1). Interestingly, subtilis clade accommodated significantly higher abundance of BGCs in another polyketide synthase (PKSother; 2.0 per genome vs. 0.0–1.1 per genome) and PKS-NRPS Hybrids (0.7 vs. 0.0–0.2) classes, as compared with the three other clades (Supplementary Table 1); while cereus clade had more BGCs in RiPPs than other clades on average (Supplementary Table 1). Overall, the profile of BGC products and classification was generally consistent with the phylogenetic tree (Supplementary Fig. 3).Fig. 2: Biosynthetic gene cluster (BGC) distribution is correlated with phylogeny in the genus Bacillus.a The numbers of BGCs in the 4268 Bacillus genomes from different clades as defined by antiSMASH15. In the violin plot, the centre line represents the median, violin edges show the 25th and 75th percentiles, and whiskers extend to 1.5× the interquartile range. b Hierarchal clustering among the 545 representative Bacillus genomes based on the abundance of the different biosynthesis gene cluster families (GCFs). Each column represents a GCF, which was classified through BiG-SCAPE by calculating the Jaccard index (JI), adjacency index (AI), and domain sequence similarity (DSS) of each BGC28; the color bar on the top of the heatmap represents the BGC class of each GCF, where PKS includes classes of PKSother and PKSI, PKS-NRPS means PKS-NRPS Hybrids, Others includes classes of saccharides, terpene, and others. Each row represents a Bacillus genome, and the abundance of each GCF in different genomes is shown in the heatmap. The left tree was constructed based on the distribution pattern of GCFs, which showes a similar pattern to the phylogram in Fig. 1. c The correlation between the BGC and phylogenetic distance of the 545 representative Bacillus genomes (P  More

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Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig, GermanyAmber Hartman Scholz, Rodrigo Sara, Scarlett Sett, Andrew Lee Hufton & Jörg OvermannLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, GermanyJens FreitagNatural History Museum, London, UKChristopher H. C. LyalOne Planet Solutions, Montpellier, FranceRodrigo SaraUniversidad de los Andes, Bogotá, ColombiaMartha Lucia CepedaPlentzia Marine Station (PiE-UPV/EHU), European Marine Biological Resource Centre – Spain (EMBRC-Spain), Plentzia, SpainIbon CancioEthiopian Biotechnology Institute, Addis Ababa, EthiopiaYemisrach Abebaw & Kassahun TesfayeNational Academy of Agricultural Science and Global Plant Council, New Delhi, IndiaKailash BansalNational Council of Scientific Research and Technologies (NCSRT), Algiers, AlgeriaHalima BenbouzaMinistry of Agriculture, Livestock, Fisheries and Cooperatives, Nairobi, KenyaHamadi Iddi BogaInstitut Pasteur, Paris, FranceSylvain Brisse, Anne-Caroline Deletoille & Raquel Hurtado-OrtizSchool of Biosciences, Cardiff University, Cardiff, UKMichael W. BrufordWellcome Sanger Institute, Hinxton, UKHayley Clissold & David NicholsonEuropean Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Hinxton, UKGuy CochraneGlobal Genome Initiative, Smithsonian National Museum of Natural History, Washington, DC, USAJonathan A. CoddingtonAlexander von Humboldt Biological Resources Research Institute, Bogota, ColombiaFelipe García-CardonaSouth African National Biodiversity Institute, Cape Town, South AfricaMichelle Hamer, Jessica da Silva & Krystal A. TolleyUniversity of Nairobi, Nairobi, KenyaDouglas W. MianoInstituto Tecnologico Vale (ITV), Belem, BrazilGuilherme OliveiraMinistry of Environment and Sustainable Development, Bogota, ColombiaCarlos Ospina BravoUniversity of Lethbridge, Lethbridge, CanadaFabian RohdenNatural History Museum of Denmark, Copenhagen, DenmarkOle SebergUniversity of Freiburg, Freiburg, GermanyGernot SegelbacherNational Centre for Cell Science, Pune, IndiaYogesh ShoucheMariano Galvez University, Guatemala City, GuatemalaAlejandra Sierra National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USAIlene Karsch-MizrachiCentre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South AfricaJessica da Silva & Krystal A. TolleyUniversity of the Philippines Los Banos, Laguna, PhilippinesDesiree M. HauteaFundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, BrazilManuela da SilvaNational Institute of Genetics, Mishima, JapanMutsuaki SuzukiInstitute of Biotechnology, Addis Ababa University, Addis Ababa, EthiopiaKassahun TesfayeCentre for Tropical Livestock Genetics and Health (CTLGH) – International Livestock Research Institute (ILRI), Nairobi, KenyaChristian Keambou TiamboMurdoch University, Murdoch, AustraliaRajeev VarshneyCorporación CorpoGen, Bogotá, ColombiaMaría Mercedes ZambranoTechnical University of Braunschweig, Braunschweig, GermanyJörg OvermannConceptualization: A.H.S., J.F., C.H.C.L., R.S., M.L.C., I.C., S.S., Y.A., K.B., H.B., H.I.B., S.Y., M.W.B., H.C., G.C., J.A.C., A.D., F.G.C., M.H., R.H.O., D.W.M., G.O., C.O.B., F.B., O.S., G.S., Y.S., A.S., J.d.S., M.d.S., M.S., K.T., K.A.T., M.M.Z., and J.O. Visualization: J.O., I.C., S.S., R.S., C.H.C.L., G.C., and A.H.S. Funding acquisition: A.H.S., J.F., and J.O. Writing—original draft: A.H.S., R.S., M.L.C., C.H.C.L., I.C., and S.S. Writing—review & editing: A.H.S., J.F., C.H.C.L., R.S., M.L.C., I.B., S.S., A.L.H., D.N., M.d.S., S.B., M.M.Z., O.S., K.T., K.A.T., R.H.O., J.d.S., C.K.T., R.V., J.O., D.H., and I.K.M. More