Determination of Soil Contamination at the Wildland-Urban Interface after the 2021 Marshall Fire in Colorado, USA.

Wildfires at the wildland-urban interface (WUI) are increasingly common. The impacts of such events are likely distinct from those that occur strictly in wildland areas, as we would expect an elevated likelihood of soil contamination due to the combustion of anthropogenic materials. We evaluated the impacts of a wildfire at the WUI on soil contamination, sampling soils from residential and nonresidential areas located inside and outside the perimeter of the 2021 Marshall Fire in Colorado, USA. We found that fire-affected residential properties had elevated concentrations of some heavy metals (including Zn, Cu, Cr, and Pb), but the concentrations were still below levels of likely concern, and we observed no corresponding increases in concentrations of polycyclic aromatic hydrocarbons (PAHs). The postfire increases in metal concentrations were not generally observed in the nonresidential soils, highlighting the importance of combustion of anthropogenic materials for potential soil contamination from wildfires at the WUI. While soil contamination from the 2021 Marshall Fire was lower than expected, and likely below the threshold of concern for human health, our study highlights some of the challenges that need to be considered when assessing soil contamination after such fires.

Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration.

Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.

The influence of disturbance scale on the natural recovery of biological soil crusts on the Colorado Plateau.

Up to 35% of global drylands have experienced degradation due to anthropogenic impacts, including physical disturbances like trampling and soil removal. These physical disturbances can result in the loss of soil communities known as biological soil crusts (biocrusts) and the important functions they provide, such as soil stability and fertility. The reestablishment of biocrust organisms after disturbance is determined by many factors, including propagule availability, climate, and vascular plant community structure. The role of these factors in natural recovery may be intensified by the extent (or size) of a disturbance. For example, large disturbances can result in reduced propagule availability or enhanced erosion, which impact both the dispersal and establishment of biocrust organisms on disturbed soils, leading to a slower natural recovery. To test how disturbance extent impacts biocrust's natural recovery, we installed four disturbance extents by completely removing biocrust from the mineral soil in plots ranging from 0.01 m2 to 1 m2 and measured productivity and erosion resistance. We found that small disturbance extents did not differ in chlorophyll a content, total exopolysaccharide content, or soil stability after 1.5 years of natural recovery. However, the concentration of glycocalyx exopolysaccharide was higher in the smallest disturbances after the recovery period. Our results indicate that disturbances <1 m2 in scale recover at similar rates, with soil stability returning to high levels in just a few years after severe disturbance. Our findings align with prior work on biocrust natural recovery in drylands and highlight the opportunity for future work to address (1) cyanobacteria, moss, and lichen propagule dispersal; (2) rates and mechanisms of biocrust succession; and (3) the role of wind or water in determining biocrust colonization patterns as compared to lateral growth.

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil.

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus.

Wastewater microbial communities are not static and can vary significantly across time and space, but this variation and the factors driving the observed spatiotemporal variation often remain undetermined. We used a shotgun metagenomic approach to investigate changes in wastewater microbial communities across 17 locations in a sewer network, with samples collected from each location over a 3-week period. Fecal material-derived bacteria constituted a relatively small fraction of the taxa found in the collected samples, highlighting the importance of environmental sources to the sewage microbiome. The prokaryotic communities were highly variable in composition depending on the location within the sampling network, and this spatial variation was most strongly associated with location-specific differences in sewage pH. However, we also observed substantial temporal variation in the composition of the prokaryotic communities at individual locations. This temporal variation was asynchronous across sampling locations, emphasizing the importance of independently considering both spatial and temporal variation when assessing the wastewater microbiome. The spatiotemporal patterns in viral community composition closely tracked those of the prokaryotic communities, allowing us to putatively identify the bacterial hosts of some of the dominant viruses in these systems. Finally, we found that antibiotic resistance gene profiles also exhibit a high degree of spatiotemporal variability, with most of these genes unlikely to be derived from fecal bacteria. Together, these results emphasize the dynamic nature of the wastewater microbiome, the challenges associated with studying these systems, and the utility of metagenomic approaches for building a multifaceted understanding of these microbial communities and their functional attributes. IMPORTANCE Sewage systems harbor extensive microbial diversity, including microbes derived from both human and environmental sources. Studies of the sewage microbiome are useful for monitoring public health and the health of our infrastructure, but the sewage microbiome can be highly variable in ways that are often unresolved. We sequenced DNA recovered from wastewater samples collected over a 3-week period at 17 locations in a single sewer system to determine how these communities vary across time and space. Most of the wastewater bacteria, and the antibiotic resistance genes they harbor, were not derived from human feces, but human usage patterns did impact how the amounts and types of bacteria and bacterial genes we found in these systems varied over time. Likewise, the wastewater communities, including both bacteria and their viruses, varied depending on location within the sewage network, highlighting the challenges and opportunities in efforts to monitor and understand the sewage microbiome.

Twenty Important Research Questions in Microbial Exposure and Social Equity.

Social and political policy, human activities, and environmental change affect the ways in which microbial communities assemble and interact with people. These factors determine how different social groups are exposed to beneficial and/or harmful microorganisms, meaning microbial exposure has an important socioecological justice context. Therefore, greater consideration of microbial exposure and social equity in research, planning, and policy is imperative. Here, we identify 20 research questions considered fundamentally important to promoting equitable exposure to beneficial microorganisms, along with safeguarding resilient societies and ecosystems. The 20 research questions we identified span seven broad themes, including the following: (i) sociocultural interactions; (ii) Indigenous community health and well-being; (iii) humans, urban ecosystems, and environmental processes; (iv) human psychology and mental health; (v) microbiomes and infectious diseases; (vi) human health and food security; and (vii) microbiome-related planning, policy, and outreach. Our goal was to summarize this growing field and to stimulate impactful research avenues while providing focus for funders and policymakers.

From the ground up: biotic and abiotic features that set the course from genes to ecosystems.

Spatial variation in cone serotiny in Rocky Mountain lodgepole pine (Pinus contorta ssp. latifolia) across Yellowstone National Park influences initial pine recruitment after stand-replacing fire with tremendous population, community, and ecosystem consequences. A previous study showed that much of the spatial variation in serotiny results from the balance of selection arising from high frequencies of fire favoring serotiny countered by opposing selection exerted by American red squirrels (Tamiasciurus hudsonicus) as seed predators. This earlier study, however, assumed stable local red squirrel densities over multiple generations of pines. Here, we examine environmental properties that might contribute to long-term stability in the densities of red squirrels among sites. We found that the amount of clay in the soil, an indicator of plant and fungal growth-the latter an important food resource for red squirrels-and the coefficient of variation (CV) in diameter at breast height (DBH) of forest trees together account for a substantial amount of variation in red squirrel density. Soil development occurs over very long time scales, and thus, intersite variation in the amount of clay is unlikely to shift across pine generations. However, CV of DBH and squirrel density increase with stand age, which acts to amplify selection against serotiny with increasing interfire interval. Regardless, much of the variation in the CV of DBH is accounted for by soil bulk density, mean annual temperature, and surface curvature, which are unlikely to vary in their relative differences among sites over time. Consequently, these soil and abiotic attributes could contribute to consistent spatial patterns of red squirrel densities from one pine generation to the next, resulting in consistent local and spatial variation in selection exerted by red squirrels against serotiny.