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Climate change and land-use legacies have caused a shift in wildfires and post-fire growing conditions. These changes have strong potential to diminish the resilience of many ecosystems, with cascading effects and feedbacks across taxa. Piñon-juniper (PJ) woodlands are a diverse and widespread forest type in the western US and are home to many obligate and semi-obligate bird species. As such, this system is ideal for understanding wildfire resilience, or lack thereof, in terms of both vegetation and wildlife associations. This study evaluated post-fire vegetation structure and associated avian communities following three wildfires; one that burned one year prior to sampling (recent fire), and two that burned approximately 25 years previously (old fires). Vegetation characteristics and the habitat use of PJ-associated bird species were compared across severely burned patches, unburned refugia, and unburned sites outside of the burn perimeter. We expected wildfire to alter vegetation and bird usage for the first few years post-fire, which we observed in our recent burns. However, even 25-years post-fire, little recovery to PJ woodland had occurred and the associated bird communities had not returned, compared to unburned areas. No piñon regeneration was observed in any burned areas and no juniper regeneration in the recent fire. Piñon seedling densities in unburned sites and refugia averaged 80 ha−1 and 151 ha−1, respectively, while juniper seedling densities were 220 ha−1 in both habitat types. Habitat use for thirteen PJ-associated species were modeled, three of which (Woodhouse’s Scrub Jay, Ash-throated Flycatcher, and Virginia’s Warbler) used all habitats. Four species (American Robin, Gray Vireo, Black-throated Gray Warbler, and Gray Flycatcher) were essentially absent from the old burn habitat, reflecting species-specific need for mature piñon or juniper trees and/or greater canopy cover. Conversely, birds that were present in the old burn habitat (including Virginia’s Warbler, Blue-gray Gnatcatcher, Woodhouse’s Scrub-jay, Ash-throated Flycatcher, and Spotted Towhee) are typically associated with habitat edges, high shrub cover, or cavity nests. Altered vegetation structure and bird habitat use in burned areas 25 years post-fire are evidence for enduring conversion to non-forest vegetation types. However, unburned refugia embedded in burned areas maintain forest attributes and support obligate bird communities, supporting ecological function and biological diversity. 

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyze 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical, and gene neighborhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.