Kalbitz, K. & Kaiser, K. Contribution of dissolved organic matter to carbon storage in forest mineral soils. J. Plant Nutr. Soil Sci. 171, 52–60 (2008).
Google Scholar
Michalzik, B. et al. Modelling the production and transport of dissolved organic carbon in forest soils. Biogeochemistry 66, 241–264 (2003).
Google Scholar
Sokol, N. W., Sanderman, J. & Bradford, M. A. Pathways of mineral-associated soil organic matter formation: Integrating the role of plant carbon source, chemistry, and point of entry. Glob. Change Biol. 25, 12–24 (2019).
Google Scholar
Roth, V.-N. et al. Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nat. Geosci. https://doi.org/10.1038/s41561-019-0417-4 (2019).
Google Scholar
Jones, O. A. H. et al. Metabolomics and its use in ecology: Metabolomics in ecology. Austral Ecol. 38, 713–720 (2013).
Gołębiewski, M. et al. Rapid microbial community changes during initial stages of pine litter decomposition. Microb. Ecol. 77, 56–75 (2019).
Google Scholar
Chomel, M. et al. Plant secondary metabolites: A key driver of litter decomposition and soil nutrient cycling. J. Ecol. 104, 1527–1541 (2016).
Purahong, W., Wubet, T., Krüger, D. & Buscot, F. Molecular evidence strongly supports deadwood-inhabiting fungi exhibiting unexpected tree species preferences in temperate forests. ISME J. 12, 289–295 (2018).
Djukic, I. et al. Early stage litter decomposition across biomes. Sci. Total Environ. 628–629, 1369–1394 (2018).
Google Scholar
Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010).
Google Scholar
Wu, Y., Zeng, J., Zhu, Q., Zhang, Z. & Lin, X. pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution. Sci. Rep. 7, 40093 (2017).
Google Scholar
Griffiths, R. I. et al. The bacterial biogeography of British soils: Mapping soil bacteria. Environ. Microbiol. 13, 1642–1654 (2011).
Google Scholar
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).
Google Scholar
Büttner, H. et al. Bacterial endosymbionts protect beneficial soil fungus from nematode attack. Proc. Natl. Acad. Sci. USA 118, e2110669118 (2021).
Google Scholar
Lucas, J. M., Gora, E., Salzberg, A. & Kaspari, M. Antibiotics as chemical warfare across multiple taxonomic domains and trophic levels in brown food webs. Proc. R. Soc. B 286, 20191536 (2019).
Google Scholar
Goldbeck, O. et al. Establishing recombinant production of pediocin PA-1 in Corynebacterium glutamicum. Metab. Eng. 68, 34–45 (2021).
Google Scholar
Wu, X. et al. Microbial interactions with dissolved organic matter drive carbon dynamics and community succession. Front. Microbiol. 9, 1234 (2018).
Google Scholar
D’Andrilli, J., Junker, J. R., Smith, H. J., Scholl, E. A. & Foreman, C. M. DOM composition alters ecosystem function during microbial processing of isolated sources. Biogeochemistry 142, 281–298 (2019).
Benk, S. A. et al. Fueling diversity in the subsurface: Composition and age of dissolved organic matter in the critical zone. Front. Earth Sci. 7, 296 (2019).
Google Scholar
Marschner, P., Umar, S. & Baumann, K. The microbial community composition changes rapidly in the early stages of decomposition of wheat residue. Soil Biol. Biochem. 43, 445–451 (2011).
Google Scholar
Badri, D. V., Zolla, G., Bakker, M. G., Manter, D. K. & Vivanco, J. M. Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol. 198, 264–273 (2013).
Google Scholar
Kohlhepp, B. et al. Pedological and hydrogeological setting and subsurface flow structure of the carbonate-rock CZE Hainich in western Thuringia, Germany. Hydrol. Earth Syst. Sci. https://doi.org/10.5194/hess-2016-374 (2016).
Dittmar, T., Koch, B. P., Hertkorn, N. & Kattner, G. A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater. Limnol. Oceanogr. 6, 230–235 (2008).
Google Scholar
Simon, C., Roth, V.-N., Dittmar, T. & Gleixner, G. Molecular signals of heterogeneous terrestrial environments identified in dissolved organic matter: A comparative analysis of orbitrap and ion cyclotron resonance mass spectrometers. Front. Earth Sci. 6, 138 (2018).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Herlemann, D. P. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).
Google Scholar
Kumar, S. et al. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol. Ecol. 94, 10 (2018).
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).
Google Scholar
Taubert, M. et al. Tracking active groundwater microbes with D 2 O labelling to understand their ecosystem function: Tracking active groundwater microbes. Environ. Microbiol. 20, 369–384 (2018).
Google Scholar
Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-596 (2013).
Google Scholar
Lohmann, P. et al. Function is what counts: How microbial community complexity affects species, proteome and pathway coverage in metaproteomics. Expert Rev. Proteomics 17, 163–173 (2020).
Google Scholar
Starke, R. et al. Candidate brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer. J. Proteomics 152, 153–160 (2017).
Google Scholar
R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2019).
Oksanen, J. et al. vegan: Community Ecology Package (Springer, 2018).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Google Scholar
Zoppi, J., Guillaume, J.-F., Neunlist, M. & Chaffron, S. MiBiOmics: an interactive web application for multi-omics data exploration and integration. BMC Bioinform. 22, 6 (2021).
Adler, D. & Murdoch, D. rgl: 3D Visualization Using OpenGL (Springer, 2019).
Aßhauer, K. P., Wemheuer, B., Daniel, R. & Meinicke, P. Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data: Fig. 1. Bioinformatics 31, 2882–2884 (2015).
Google Scholar
Fath, M. J. & Kolter, R. ABC transporters: Bacterial exporters. Microbiol. Rev. 57, 995 (1993).
Google Scholar
Waters, C. M. & Bassler, B. L. Quorum sensing: Cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319–346 (2005).
Google Scholar
Deutscher, J., Francke, C. & Postma, P. W. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol. Mol. Biol. Rev. 70, 939–1031 (2006).
Google Scholar
Vogt, T. Phenylpropanoid biosynthesis. Mol. Plant 3, 2–20 (2010).
Google Scholar
Polturak, G. et al. Engineered gray mold resistance, antioxidant capacity, and pigmentation in betalain-producing crops and ornamentals. PNAS 114, 9062–9067 (2017).
Google Scholar
Mille-Lindblom, C. & Tranvik, L. J. Antagonism between bacteria and fungi on decomposing aquatic plant litter. Microb. Ecol. 45, 173–182 (2003).
Google Scholar
Chopra, I. & Roberts, M. Tetracycline antibiotics: Mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol. Mol. Biol. Rev. 65, 232–260 (2001).
Google Scholar
Schiessl, K. T. et al. Phenazine production promotes antibiotic tolerance and metabolic heterogeneity in Pseudomonas aeruginosa biofilms. Nat. Commun. 10, 762 (2019).
Google Scholar
Reading, C. & Cole, M. Clavulanic acid: A beta-lactamase-inhiting beta-lactam from Streptomyces clavuligerus. Antimicrob. Agents Chemother. 11, 852–857 (1977).
Google Scholar
Šnajdr, J. et al. Transformation of Quercus petraea litter: Successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition: Transformation of Quercus petraea litter. FEMS Microbiol. Ecol. 75, 291–303 (2011).
Google Scholar
Voříšková, J. & Baldrian, P. Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J. 7, 477–486 (2013).
Google Scholar
Buresova, A. et al. Succession of microbial decomposers is determined by litter type, but site conditions drive decomposition rates. Appl. Environ. Microbiol. 85, e01760-19 (2019).
Google Scholar
Hopwood, D. A. Streptomyces in Nature and Medicine: The Antibiotic Makers (Oxford University Press, 2007).
Anaya-López, J. L., López-Meza, J. E. & Ochoa-Zarzosa, A. Bacterial resistance to cationic antimicrobial peptides. Crit. Rev. Microbiol. 39, 180–195 (2013).
Google Scholar
Lindner, K. R., Bonner, D. P. & Koster, W. H. Monobactams. Kirk-Othmer Encyclopedia of Chemical Technology (Wiley, 2000). https://doi.org/10.1002/0471238961.1315141512091404.a01.
Google Scholar
Eustáquio, A. S. et al. Novobiocin biosynthesis: Inactivation of the putative regulatory gene novE and heterologous expression of genes involved in aminocoumarin ring formation. Arch. Microbiol. 180, 25–32 (2003).
Google Scholar
Banerjee, S. et al. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol. Biochem. 97, 188–198 (2016).
Google Scholar
Taubert, M., Stähly, J., Kolb, S. & Küsel, K. Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PLoS ONE 14, e0212937 (2019).
Google Scholar
Wallenstein, M. D., Hess, A. M., Lewis, M. R., Steltzer, H. & Ayres, E. Decomposition of aspen leaf litter results in unique metabolomes when decomposed under different tree species. Soil Biol. Biochem. 42, 484–490 (2010).
Google Scholar
Backlund, I. et al. Extractive profiles of different lodgepole pine (Pinus contorta) fractions grown under a direct seeding-based silvicultural regime. Ind. Crops Prod. 58, 220–229 (2014).
Google Scholar
Source: Ecology - nature.com