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Abstract BackgroundMicroorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California’s largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022. ResultsWe observed that the water column microbiome significantly varied by season (R² = 0.59,P = 0.003). Temperature (R² = 0.27,P = 0.004), dissolved organic matter (R² = 0.13,P = 0.004), and dissolved oxygen (R² = 0.089,P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons. ConclusionsOur work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea’s sulfur cycle, dust proliferation, and respiratory distress experienced by the local population. 

IntroductionThe 1980 eruption of Mount St. Helens had devastating effects above and belowground in forested montane ecosystems, including the burial and destruction of soil microbes. Soil microbial propagules and legacies in recovering ecosystems are important for determining post-disturbance successional trajectories. Soil microorganisms regulate nutrient cycling, interact with many other organisms, and therefore may support successional pathways and complementary ecosystem functions, even in harsh conditions. Historic forest management methods, such as old-growth and clearcut regimes, and locations of historic short-term gopher enclosures (Thomomys talpoides), to evaluate community response to forest management practices and to examine vectors for dispersing microbial consortia to the surface of the volcanic landscape. These biotic interactions may have primed ecological succession in the volcanic landscape, specifically Bear Meadow and the Pumice Plain, by creating microsite conditions conducive to primary succession and plant establishment. Methods and resultsUsing molecular techniques, we examined bacterial, fungal, and AMF communities to determine how these variables affected microbial communities and soil properties. We found that bacterial/archaeal 16S, fungal ITS2, and AMF SSU community composition varied among forestry practices and across sites with long-term lupine plots and gopher enclosures. The findings also related to detected differences in C and N concentrations and ratios in soil from our study sites. Fungal communities from previously clearcut locations were less diverse than in gopher plots within the Pumice Plain. Yet, clearcut meadows harbored fewer ancestral AM fungal taxa than were found within the old-growth forest. DiscussionBy investigating both forestry practices and mammals in microbial dispersal, we evaluated how these interactions may have promoted revegetation and ecological succession within the Pumice Plains of Mount St. Helens. In addition to providing evidence about how dispersal vectors and forest structure influence post-eruption soil microbiomes, this project also informs research and management communities about belowground processes and microbial functional traits in facilitating succession and ecosystem function. 

Leaf-cutter ants (LCAs) are widely distributed and alter the physical and biotic architecture above and below ground. In neotropical rainforests, they create aboveground and belowground disturbance gaps that facilitate oxygen and carbon dioxide exchange. Within the hyperdiverse neotropical rainforests, arbuscular mycorrhizal (AM) fungi occupy nearly all of the forest floor. Nearly every cubic centimeter of soil contains a network of hyphae of Glomeromycotina, fungi that form arbuscular mycorrhizae. Our broad question is as follows: how can alternative mycorrhizae, which are—especially ectomycorrhizae—essential for the survival of some plant species, become established? Specifically, is there an ant–mycorrhizal fungus interaction that facilitates their establishment in these hyperdiverse ecosystems? In one lowland Costa Rican rainforest, nests of the LCAAtta cephalotescover approximately 1.2% of the land surface that is broadly scattered throughout the forest. On sequencing the DNA from soil organisms, we found the inocula of many AM fungi in their nests, but the nests also contained the inocula of ectomycorrhizal, orchid mycorrhizal, and ericoid mycorrhizal fungi, includingScleroderma sinnamariense, a fungus critical toGnetum leyboldii, an obligate ectomycorrhizal plant. When the nests were abandoned, new root growth into the nest offered opportunities for new mycorrhizal associations to develop. Thus, the patches created by LCAs appear to be crucial sites for the establishment and survival of shifting mycorrhizal plant–fungal associations, in turn facilitating the high diversity of these communities. A better understanding of the interactions of organisms, including cross-kingdom and ant–mycorrhizal fungal interactions, would improve our understanding of how these ecosystems might tolerate environmental change. 

Soils are the largest source of atmospheric nitrous oxide (N₂O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N₂O-producing process, yet, among the largest N₂O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N₂O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N₂O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ¹⁵N^bulk= 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N₂O emissions by 59%. Our results suggest that despite extreme environmental conditions—months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%—bacterial denitrifiers can account for most of the N₂O emitted when dry soils are wetted. 

Soil ammonia (NH3) emissions are seldom included in ecosystem nutrient budgets; however, they may represent substantial pathways for ecosystem nitrogen (N) loss, especially in arid regions where hydrologic N losses are comparatively small. To characterize how multiple factors affect soil NH3 emissions, we measured NH3 losses from 6 dryland sites along a gradient in soil pH, atmospheric N deposition, and rainfall. We also enriched soils with ammonium (NH4+), to determine whether N availability would limit emissions, and measured NH3 emissions with passive samplers in soil chambers following experimental wetting. Because the volatilization of NH3 is sensitive to pH, we hypothesized that NH3 emissions would be higher in more alkaline soils and that they would increase with increasing NH4+ availability. Consistent with this hypothesis, average soil NH3 emissions were positively correlated with average site pH (R2 = 0.88, P = 0.004), ranging between 0.77 ± 0.81 µg N-NH3 m−2 h−1 at the least arid and most acidic site and 24.2 ± 16.0 µg N-NH3 m−2 h−1 at the most arid and alkaline site. Wetting soils while simultaneously adding NH4+ increased NH3 emissions from alkaline and moderately acidic soils (F1,35 = 14.7, P < 0.001), suggesting that high N availability can stimulate NH3 emissions even when pH is less than optimal for NH3 volatilization. Thus, both pH and N availability act as proximate controls over NH3 emissions suggesting that these N losses may limit how much N accumulates in arid ecosystems. 

Although the Salton Sea was once a thriving destination for humans and wildlife, it has now degraded to the point of ecosystem collapse. Increases in local dust emissions have introduced aeolian (wind-blown) microorganisms that travel, along with contaminants and minerals, into the atmosphere, detrimentally impacting inhabitants of the region. Proliferation of certain microbial groups in regions of the Sea may have a disproportionate impact on local ecological systems. Yet, little is known about how the biogeochemical processes of this drying lakebed influence microbial community composition and dispersal. To elucidate how these microorganisms contribute, and adapt, to the Sea's volatile conditions, we synthesize research on three niche-specific microbiomes — exposed lakebed (playa), the Sea, and aeolian — and highlight modern molecular techniques, such as metagenomics, coupled with physical science methodologies, including transport modeling, to predict how the drying lakebed will affect microbial processes. We argue that an explicit consideration of microbial groups within this system is needed to provide vital information about the distribution and functional roles of ecologically pertinent microbial groups. Such knowledge could help inform regulatory measures aimed at restoring the health of the Sea's human and ecological systems. 

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.