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Abstract Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning—the combustion of logging residue on the forest floor—is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change. 

The plasticity of some coral-associated microbial communities under stressors like warming and ocean acidification suggests the microbiome has a role in the acclimatization of corals to future ocean conditions. Here, we evaluated the acclimatization potential of coral-associated microbial communities of four Hawaiian coral species (Porites compressa,Porites lobata,Montipora capitata, andPocillopora acuta) over 22-month mesocosm experiment. The corals were exposed to one of four treatments: control, ocean acidification, ocean warming, or combined future ocean conditions. Over the 22-month study, 33–67% of corals died or experienced a loss of most live tissue coverage in the ocean warming and future ocean treatments while only 0–10% died in the ocean acidification and control. Among the survivors, coral-associated microbial communities responded to the chronic future ocean treatment in one of two ways: (1) microbial communities differed between the control and future ocean treatment, suggesting the potential capacity for acclimatization, or (2) microbial communities did not significantly differ between the control and future ocean treatment. The first strategy was observed in bothPoritesspecies and was associated with higher survivorship compared toM.capitataandP.acutawhich exhibited the second strategy. Interestingly, the microbial community responses to chronic stressors were independent of coral physiology. These findings indicate acclimatization of microbial communities may confer resilience in some species of corals to chronic warming associated with climate change. However,M.capitatagenets that survived the future ocean treatment hosted significantly different microbial communities from those that died, suggesting the microbial communities of the survivors conferred some resilience. Thus, even among coral species with inflexible microbial communities, some individuals may already be tolerant to future ocean conditions. These findings suggest that coral-associated microbial communities could play an important role in the persistence of some corals and underlie climate change-driven shifts in coral community composition. 

Abstract Background Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK ( S ooner T rend A nadarko Basin, C anadian and K ingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.