Data for "Stable states in an unstable landscape: microbial resistance at the front line of climate change"

Datasets used in analysis for "Stable states in an unstable landscape: microbial resistance at the front line of climate change" (https://doi.org/10.1101/2025.02.07.636677). It can be used to regenerate the figures using code on Github. Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. Because the rapid thaw of permafrost peatlands makes a very large store of soil carbon available to microbial metabolism, understanding microbiome dynamics in these systems is particularly urgent. We quantified microbial warming response over seven years across three habitats in a thawing permafrost peatland, using large-scale multi-omics data. We integrated analyses of organisms (via taxonomy), functions (via metabolic pathways and proteins), and community organization (via network structure and ecological assembly) to deeply characterize response mechanisms. We consistently found a pattern of within-habitat microbiome stability, with virtually no signal of gradual change in the warming period studied. The resistance to change appeared bolstered by habitat-specific dispersal processes and community-level functional redundancy, particularly via versatile carbon generalists. Our findings also reveal key genome-inferred metabolic processes that underlie microbiome stability. Together, our results highlight the importance of understanding the limits of these stabilizing processes and suggest that future research should reorient towards critical habitat transitions. Non-author contributions This study has been made possible by data provided by Abisko Scientific Research Station and the Swedish Infrastructure for Ecosystem Science (SITES) as well as the Swedish Polar Research Secretariat. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. A portion of this analysis and non-monetary technical support was also provided through the U.S. Department of Energy user facilities programs. Computational work was supported in part by an allocation of computing time from the Ohio Supercomputer Center. Lastly, we thank contracted science artist Elena Hartley for co-development of Fig. 6. Funding We thank the many funding sources of this work, including: US National Science Foundation, Biology Integration Institutes Program, Award # 2022070 (VIR and RKV, with SH, MMT, GWT, BW, JE, SCB, and the EMERGE Institute Coordinators) Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research (BER), grants DE-SC0004632, DE-SC0010580 and DE-SC0016440 (SRS and VIR, with GWT, MMT). Associated with the third of these was a BER Support Science award (Proposal #503530 DOI: 10.46936/10.25585/60001148) for nucleic acid sequencing for a portion of these samples, conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. US National Science Foundation MacroSystems Program, Award # NSF EF 1241037 (RV). US National Science Foundation Research for Undergraduates Program, the Northern Ecosystems Research for Undergraduates, Award # NSF REU EAR 1063037 (RV) Nucleic acid sequencing and and dissolved organic matter fourier transform ion cyclotron resonance mass spectrometry were partially supported by a Facilities Integrating Collaborations for User Science (FICUS) awards, DOI: 10.46936/fics.proj.2016.49521/60006018 and 503547, which used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Office of Biological and Environmental Research and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). SITES is supported by the Swedish Research Council’s grant 4.3-2021-00164