Published paper: The global topsoil microbiome
I’m really late at this ball for a number of reasons, but last week Nature published our paper on the structure and function of the global topsoil microbiome (1). This paper has a long story, but in short I got contacted by Mohammad Bahram (the first author) about two years ago about a project using metagenomic sequencing to look at a lot of soil samples for patterns of antibiotic resistance gene abundances and diversity. The project had made the interesting discovery that resistance gene abundances were linked to the ratio of fungi and bacteria (so that more fungi was linked to more resistance genes). During the following year, we together worked on deciphering these discoveries, which are now published in Nature. The paper also deals with the taxonomic patterns linked to geography (1), but as evident from the above, my main contribution here has been on the antibiotic resistance side.
In short, we find that:
- Bacterial diversity is highest in temperate habitats, and lower both closer to the equator and the poles
- For bacteria, the diversity of biological functions follows the same pattern, but for fungi, the functional diversity is higher closer to the poles and the equator
- Higher abundance of fungi is linked to higher abundance and diversity of antibiotic resistance genes. Specifically, this is related to known antibiotic producing fungal lineages, such as Penicillium and Oidiodendron. There also seems to be a link between the Actinobacteria, encompassing the antibiotic-producing bacterial genus of Streptomyces and higher resistance gene diversity.
- Similar relationships between the fungus-like Oomycetes and resistance genes was also found in ocean samples from the Tara Oceans project (2)
The results of this study indicate that both environmental filtering and niche differentiation determine soil microbial composition, and that the role of dispersal limitation is minor at this scale. Soil pH and precipitation seems to be the strongest drivers of community composition. Furthermore, we interpret our data to reveal that inter-kingdom antagonism is important in structuring microbial communities. This speaks against the notion put forward that antibiotic resistance genes might not have a resistance function in natural settings (3). That said, the most likely explanation here is probably a bit of both warfare and repurposing of genes. Soil seems to be the largest untapped source of resistance genes for human pathogens (4), and the finding that natural antagonism may be driving resistance gene diversification and enrichment may be important for future management of environmental antibiotic resistance (5,6).
It was really great to work with Mohammad and his team, and I sure hope that we will collaborate again in the future. The entire paper can be found in the issue of Nature coming out this week, and is already online at Nature’s website.
- Bahram M°, Hildebrand F°, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P: Structure and function of the global topsoil microbiome. Nature, 560, 233–237 (2018). doi: 10.1038/s41586-018-0386-6
- Sunagawa S et al. Structure and function of the global ocean microbiome. Science 348, 6237, 1261359 (2015). doi: 10.1126/science.1261359
- Aminov RI: The role of antibiotics and antibiotic resistance in nature. Environmental Microbiology, 11, 12, 2970-2988 (2009). doi: 10.1111/j.1462-2920.2009.01972.x
- Bengtsson-Palme J: The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants – but not always. Microbiome, 6, 125 (2018). doi: 10.1186/s40168-018-0508-2
- Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053
- Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Ploy M-C, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson A-S: Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environment International, 117, 132–138 (2018).