Search

Air pollution, containing fossil fuel-related volatile organic compounds (VOCs), constitutes a major problem in most urban areas. Worldwide, more people die from exposure to air pollution than from malaria and HIV infection together. Many years of research show that plant–microbe interactions can be exploited to significantly enhance phytoremediation of contaminated environments. Microorganisms living on plant leaves constitute promising candidates to detoxify harmful VOCs and promote plant growth. Hedera helix, an evergreen plant known for its hardiness and climbing ability, proves to be an excellent host species in the context of phytoremediation of air pollution. We employed 16S rRNA gene amplicon-based metagenomics to characterize the taxonomic structure of phyllospheric microbial communities associated with H. helix. Further, we investigated 33 bacterial isolates from 8 different genera using culture-dependent approaches and whole genome sequencing. Our results indicate that the relative composition of the H. helix phyllobiome is similar to that of the model plant Arabidopsis thaliana. The presence of pathways related to detoxification of fossil fuel-related VOCs could be confirmed by genome-level analyses of bacterial isolates showing a high in vitro capacity to metabolize selected VOCs and promote plant growth. We provide an integrated description of the H. helix phyllobiome, including the identification of interesting bacteria with significant potential as inoculants in phytoremediation approaches. Het Fonds voor Wetenschappelijk Onderzoek – Vlaanderen (FWO)

Air pollution, containing fossil fuel-related volatile organic compounds (VOCs), constitutes a major problem in most urban areas. According to recent data, more people die from exposure to air pollution than from malaria and HIV infection together. Many years of research show that plant–microbe interactions can be exploited to significantly enhance phytoremediation of contaminated environments. Microorganisms living on plant leaves constitute promising candidates to detoxify harmful VOCs and promote plant growth. Hedera helix, an evergreen plant known for its hardiness and climbing ability, proves to be an excellent host species in the context of phytoremediation of air pollution. We employed 16S rRNA gene amplicon-based metagenomics and real-time PCR to characterize the taxonomic structure of phyllospheric microbial communities associated with H. helix, and compared the communities present at polluted high-traffic locations with non-polluted sites. Further, we investigated bacterial isolates using culture-dependent approaches and sequenced the genomes of promising bacteria with regard to phytoremediation applications. Our results indicate that Actinobacteria, Firmicutes and Betaproteobacteria are more abundantly present on H. helix leaves in a polluted environment. Moreover, the relative composition of the H. helix phyllobiome appears to be similar to that of the model plant Arabidopsis thaliana. We further show that air pollution increases the prevalence of bacterial functional traits affiliated to plant growth and detoxification of fossil fuel-related VOCs. The presence of relevant pathways could be confirmed by genome-level analyses of bacterial isolates showing a high in vitro capacity to metabolize selected VOCs and promote plant growth. In conclusion, an integrated description of the H. helix phyllobiome is presented, including the identification of interesting bacteria with significant potential as inoculants in phytoremediation approaches. This work is supported by the Hasselt University Methusalem project 08M03VGRJ

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. The work (proposal DOI[s]: https://doi.org/10.46936/10.25585/60001024; https://doi.org/10.46936/10.25585/60000886; https://doi.org/10.46936/10. 25585/60001401; https://doi.org/10.46936/10.25585/60001087; https:// doi.org/10.46936/10.25585/60001079; https://doi.org/10.46936/10.25585/ 60001044) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no. DE-AC02-05CH11231. Design and synthesis of peptide constructs were supported by the Biosystems Design program (DOE Office of Science contract DE-SC0018260) and the US Department of Energy Joint Genome Institute (DOE Office of Science contract DEAC02-05CH1123), respectively. Characterization of the peptide was supported by the Secured Biosystem Design project entitled ‘‘Rapid Design and Engineering of Smart and Secure Microbiological Systems’’ (DOE Office of Science contract DE-AC02-05CH1123). We thank the following researchers for their support of this study by providing free use of their public genome data: Kristen De-Angelis, Grace Pold, Mallory Choudoir, Camila Carlos-Shanley, Paul Carini, H. Corby C. Kistler, James Elkins, Javier A. Izquierdo, Dimitris Hatzinikolaou, Daniel Schachtman, Paul R. Jensen, Aindrila Mukhopadhyay, John Vogel, Carolin Frank, Paul M. D’Agostino, Ann M. Hirsch, Satoshi Yuzawa, Regina Lamendella, Bernhard Fuchs, Dale Pelletier, Laila P. Partida-Martinez, Cameron Currie, Seth De-Bolt, Jeff Dangl, David Mead, Susannah Tringe, David A. Baltrus, Seung Bum Kim, Linda Kinkel, Kelly Wrighton, William Mohn, Ludmila Christoserdova, Sarah Lebeis, Janet Janssen, Sandra Baena Garzon, and Nicholas Coleman. Special thanks to Marie Louise Ballon at the JGI Communications and Outreach office for all her help with the graphical abstract and many other details.

Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies. This work was financed by the Methusalem project 08M03VGRJ and was also supported by grants to STh and NW from the Fund of Scientific Research Handers. Thanks to Prof. Dr. Geert-Jan Bex for help with setting up the Flemish Supercomputer Centre (VSC) supported by the Research Foundation Handers (FWO) in partnership with the five Flemish university associations.