The invasive terrestrial gastropod, the slug Lehmannia valentiana, is distributed throughout California. It originates from Europe and is a serious pest of gardens, plant nurseries, and greenhouses. Terrestrial slugs frequently ingest soil and plant bacteria from dead and living plant material while also picking up bacteria on their bodies and in their mucus. These bacteria can then be dispersed as they travel which could possibly cause disturbances to native soil microbial community functioning, as well as cause concern for human health or agricultural crops. Altering soil microbial community composition by slugs, such as interrupting the action of free-living microbes, altering rates of nutrient supply and the portioning of resources may be detrimental to plant communities. Horticulturalists, agronomists, and land managers are recognizing the need to control slug populations in an ecologically sound and effective manner.

Prior to this research, little was known about slug bacterial dispersal. Additionally, information regarding whole slug bacterial microbiomes is limited. This knowledge could provide valuable information for biocontrol studies. Moreover, this research provides evidence for the potential of slugs to disperse bacteria. With the advances of next-generation sequencing, focus on host-microbiome systems have expanded and now include a wider range of plants and animals, notably invertebrates. Bacteria associated with invertebrates may be ecologically significant as these microbes potentially perform many functions, including supporting overall fitness and health. Although invertebrates make excellent study models, minimal work has been conducted on characterizing bacterial associations with terrestrial slugs.

This novel research investigated an invasive California slug, L. valentiana, and documented the ability of this slug to disperse bacteria while providing critical information about its bacterial microbiome and effect on soil bacterial communities. This research may raise awareness to the adverse contributing factors slugs have in environmental and agricultural settings. Additionally, these findings fill a gap in current malacological research, provide material on new methods of slug DNA extraction, and assist in slug bacterial microbiome discovery, which could offer valuable information for future biocontrol studies.

Biological plant invasions impact the function and biodiversity of ecosystems across the globe by displacing native plant species and altering the physical and chemical soil environment. In California, invasive grasses have displaced native plants, transforming much of the endemic coastal sage scrub (CSS) to nonnative grasslands. This has occurred for several reasons including increased competitive ability of invasive grasses and long-term alterations to the soil environment, called legacy effects. Despite the magnitude of this problem, however, it is not well understood how these legacy effects have altered the soil microbial community and, indirectly, native plant restoration.

Chapter one explores how invasive plants change the abundance and diversity of three important fungal symbionts (arbuscular mycorrhizal fungi, ectomycorrhizal fungi, and fungal pathogens), as well as the implications these changes may have for ecosystem health. I finish off the chapter by discussing restoration efforts designed to ameliorate fungal legacy effects of invasive plants.

Chapter two assesses the microbial composition of soils collected from an uninvaded coastal sage scrub (CSS) community (uninvaded soil) and a nearby 10ha site from which the invasive grass, Harding grass (Phalaris aquatica L.), was removed after 11 years of growth (post-invasive soil) in order to better understand the long-term impact of invasive grasses on soil microbes. Our findings indicate that Harding grass may create microbial legacy effects in the soil that likely cause soil conditions inhibitory to the germination rate, biomass, and length of California sagebrush, but not the other two native plant species.

Chapter three seeks to understand if differences in native plant growth can be explained by biotic legacy effects and if these legacy effects can be reversed. We measure the growth of three CSS species inoculated with either uninvaded soil or sterilized uninvaded soil and planted into a site with known microbial legacy effects. Our findings indicate that differences in native plant growth can be explained by changes in the soil microbial community and that remediation of the soil microbial community through inoculation can improve restoration in post-invasive sites.

Microbial nitrogen cycling in hot desert soils is dominated by bursts of biogeochemical metabolic activity during short periods of water availability. Both edaphic traits of the soil ecosystem and the functional traits of the soil microbiome influence the transformation of nitrogen during this process. The aim of this research is to determine how soil bacteri and fungi transform mineral N and how air pollution in the form of atmospheric nitrogen deposition (N-dep) impacts nitrogen cycling. I used a set of desert field sites across a nitrogen deposition gradient in order to investigate soil microbiomes with increasing exposure to chronic atmospheric N-dep. In Chapter 1, I track bacterial and fungal communities over time in response to N addition to show patterns of community change corresponding to NO emissions. In Chapter 2, dry soils were taken from across the N-dep gradient and incubated with 15NH4 in the lab in order to stimulate nitrogen assimilation by soil bacteria. Using this heavy isotope substrate enriched nitrogen assimilating bacterial DNA with 15N, allowing me to determine the degree of growth using DNA-quantitative stable isotope probing (DNA-qSIP). I then sequenced the bacterial 16S ribosomal gene from this qSIP-processed DNA and analyzed the sequence data to calculate isotope incorporation by each bacterial species. I found that with increasing exposure to N-dep, there was a more phylogenetically diverse group of assimilators. Furthermore, assimilation of NH4 across the N-dep gradient was dominated by 5 bacterial orders: Rhizobiales, Burkholderiales, Frankiales, Cytophagales, and Sphingomonadales. In Chapter 3, rewetting experiments were performed at 4 desert field sites with increasing annual loads of N-dep in order to stimulate bacterial metabolic activity. Metagenomes were sequenced in order to determine which nitrogen cycling functional genes were present in the soil, and which genes increase in abundance during rewetting. I found that N-dep significantly altered the composition of genes related to denitrification and organic matter decomposition, although I did not find any significant patterns of gene abundance before and after rewetting. Overall, these experiments demonstrate that nitrogen deposition alters several aspects of the desert nitrogen cycle by changing the composition and gene inventory of soil bacteria.

Soil microbial communities are vital to a wide range of ecosystems, but they are poorly understood. Advances in high-throughput amplicon sequencing have enabled a greater understanding of how communities differ from each other. Previous studies have both found important variations with depth within soil profiles and across geospatial location, but few studies have examined both depth and location simultaneously. This study utilizes the Critical Zone Observatory Network to assay a total of 18 sites at a continental scale, each sampled to approximately 100 cm in 10-cm increments. Each of the approximately 180 biologically distinct samples was assessed for a variety of pedological variables including pH, particle size distribution, and nutrient composition. In addition, 16S (prokaryotic) and fungal ITS1 amplicons were sequenced to examine microbial community composition. Although previous literature has seen a marked decrease in diversity with increasing depth for 16S communities, this study shows that such soil profiles form a distinct subset, and that in many sites, there is no significant decrease in diversity with depth (termed "gradient" and "uniform" profiles here, respectively). Futhermore, while site-to-site variations tend to be important drivers of community differences, there are also strong similarities between extremely geographically distant communities that share similarities in ecological setting. In particular, soil taxonomic order and dominant vegetation types show strong correspondences with similarities between communities, but the tendency towards distinction between such groupings is overshadowed by the gradient-uniform dichotomy. This study, therefore, suggests that future work in comparisons of microbial communities across geospatial gradients needs to account for the ecological setting of selected sites, in particular accounting for soil taxonomy and vegetation. Although there are hints that the gradient-uniform dichotomy is linked to changes in soil texture and the relative availability of carbon and nitrogen, further research is required to robustly explain this distinction.

Microorganisms are ubiquitous in their distributions and are integral to global nutrient cycling. Yet, microbial metabolic strategies are niche-specific, as environmental conditions including nutrient and moisture availability, oxygen concentration, and salinity select for certain microbial adaptations. The Salton Sea, a hypersaline and eutrophic lake in Southern California, presents a unique opportunity to investigate how the environment selects for microbial survival and dispersal, which has urgent implications for both ecosystem stability and public health impacts. In Chapter 1, we explored the geochemistry of the Salton Sea sub-ecosystems (i.e., the playa, seawater, and aeolian) and how they structure their respective microbiomes. We also detail the paucity of research into these communities and describe modern methods like metagenomics and wind modeling that could be used to characterize the Salton Sea microbiomes. In Chapter 2, we examined the Salton Seawater microbiome within a water column during periods of lake stratification and turnover in 2020 and 2021. We characterized the taxonomic composition of the lake’s microbiome across seasons by sequencing the bacterial 16S rRNA gene (V3-V4) and used metagenomic sequencing to assess the community’s capacity for sulfur cycling. While microbiome composition significantly varied between seasons, halophilic, mixotrophic bacteria consistently dominated the water column. Additionally, sulfur oxidation genes were shared across depths and their relative coverage fluctuated with seasonal shifts in oxygen, sulfide, and sulfate concentrations. In Chapter 3, we used amplicon sequencing of the 16S rRNA gene (V3-V4), metagenomic sequencing, and wind geospatial data to characterize the aeolian dust microbiome and their adaptations that permit atmospheric survival and dispersal. We identified a core aeolian microbiome including bacterial genera such as Massilia, Sphingomonas, and 11 other stress-tolerant taxa. We also observed that the dust microbiome contains the necessary adaptations for persisting in dust, including UV radiation resistance genes and osmotic resistance genes, and that the distribution of these traits was driven by wind conditions. Together, these findings demonstrate that harsh environments select for microbial survival strategies, which in turn, regulate the ecosystems’ geochemistry and stability. Furthermore, this relationship structures both microbial colonization and dispersal, which may pose a danger to the public upon exposure.