Post-fire vegetation and bird habitat use in piñon-juniper woodlands

2022 Spring.Includes bibliographical references.Global climate change has caused fire activity and behavior to shift from historical norms due to hotter and drier conditions. Although the ecological effects of changing fire regimes have been explored in many systems, the resilience of some forest types, such as piñon-juniper, are often overlooked. Piñon-juniper is a dominant forest type in the western US and provides breeding habitat for many obligate or semi-obligate bird species. Similarly, this system is supported by a critical mutualism, where the regeneration and infilling of these trees is reliant on several bird species that disperse piñon pine and juniper seeds. This study aimed to assess woodland resilience by evaluating post-fire forest structure and the associated avian communities one-year and 20+ years post-fire. More specifically, seedling regeneration and the habitat use of piñon-juniper obligate bird species, semi-obligates, piñon seed dispersers, and juniper seed dispersers were compared across burned, refugia, and unburned patches. Replicate patches of each habitat type were selected within three fire locations, and 3-4 bird point count stations and 1 forest inventory plot were established in each patch. No tree regeneration was observed 1-year post-fire, and after 25 years, there were few juniper seedlings and no piñon seedlings observed in burned plots. Seedling regeneration and forest structure in refugia and unburned plots were not different, regardless of fire age. Results from occupancy models indicated that Woodhouse's Scrub-jay, a piñon seed disperser, used all habitats equally. American Robin had the highest habitat use in the recent burned patches. Obligate and semi-obligate bird species had differing responses to habitat types, with the habitat use of Ash-throated Flycatcher and Spotted Towhee not differing across habitat types, Virginia's Warbler having the highest habitat use in old burn and refugia patches, the Gray Vireo, Black-throated Gray Warbler, and Gray Flycatcher having highest habitat use in unburned, refugia, and recent burn patches, and the Blue-grey Gnatcatcher having the highest habitat use in the old burn. While there is a need for longer term studies, our work highlights that even 25 years post-fire, little tree recovery is observed and the associated bird species continue to differ, emphasizing the potential transition or long recovery time in these sensitive areas

Unraveling the functional dark matter through global metagenomics

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. 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 analyse 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 database3. 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 neighbourhood 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

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.</p