Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, our understanding of their biogeographic patterns and the processes that drive those patterns is underdeveloped. My dissertation provides a comprehensive analysis of bacterial biogeographic patterns and investigates how dispersal into soil impacts microbiome assembly. To establish global biogeographic patterns, I analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project (Chapter 1). This study compared bacterial diversity trends across habitats and provided a big-picture analysis that linked multiple smaller-scale studies. From this study, I found that soils contained the highest bacterial richness within a single sample, prompting a follow-up field experiment to study how dispersal may drive the high diversity found in soils.

Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly and diversity. Dispersal may be particularly important to leaf litter, the top layer of soil, which is exposed to microbial immigration from multiple sources and plays a key role in nutrient cycling in soils. However, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. To fill this gap, I characterized the rate and composition of bacteria dispersing into leaf litter via three dispersal routes (through the air, from nearby vegetation, and up from the bulk soil) and simultaneously quantified the impact of those routes on soil microbiomes (Chapter 2). I found that dispersal from vegetation changed the microbiome composition and functioning, driving the decomposition of leaf litter. That result led to another field experiment to characterize immigration rates and composition of microorganisms dispersing from the plant communities of two ecosystems: a grassland and a shrubland (Chapter 3). Immigrating microorganisms were strongly correlated with the local vegetation, although only within 1 m – a much shorter dispersal distance than previously assumed. Overall, my dissertation highlights the high microbial diversity found in soils and suggests that dispersal into leaf litter from local vegetation plays a central role in the assembly of soil microbiomes.

Despite our ability to characterize diverse microbial communities, we currently lack the capability to identify the mechanisms affecting a given taxon’s response to environmental conditions and its functional consequence. This problem partly stems from the common practice of characterizing microbial communities using conserved marker genes, such as the 16S rRNA region, which mask ecologically-relevant genetic and phenotypic variation. For example, most microbial studies that target the 16S rRNA region, cluster similar sequences into operational taxonomic units (OTUs) that represents millions of years of evolutionary history. My work has explored how much genetic variation may exist within these OTU designations and identified how genetic variation corresponds to phenotypic variation (overview in Chapter 1). Overall, I have focused on the ecological and evolutionary mechanisms driving environmental niche partitioning and speciation within a bacterial taxon to link genotypic variation to functional roles.

Utilizing an abundant soil bacterium, Curtobacterium, I have demonstrated that isolates within this Actinobacteria genus harbored extensive genomic diversity within a single OTU (Chapter 2) that reflected large phenotypic variation even within a single field site. Using extensive isolation efforts with the integration of genomic and metagenomic data, I have identified distinct genomic clusters that would otherwise be masked by traditional microbial analyses (Chapter 3). Further, this vast genomic diversity corresponded to distinct phenotypes denoting fine-scale niche partitioning and the emergence of bacterial ecological populations along a regional climate gradient (Chapter 4). While ecological variation may drive large-scale geographic distributions, the evolutionary mechanisms contributing to microbial speciation and diversity have remained elusive. Selection can drive microbial speciation and later divergence due to barriers to gene flow or mutational adaptations. By analyzing ecologically-similar strains, I demonstrated that Curtobacterium isolates are diverging into independent populations in a heterogeneous soil system (Chapter 5). In conclusion, my research has provided evidence that ecological and evolutionary processes both contribute to the response of bacteria to environmental conditions.

Humans harbor a diverse microbiome in their gut including a diversity of bifidobacteria species. The bacterial group bifidobacteria (genus Bifidobacterium) is fundamental to the health of humans and animals. They are inhabitants of the gastrointestinal tract, vagina, and mouth of mammals and some insects. Bifidobacteria have gained notable attention as their presence in the gut has been correlated with many health-promoting benefits. While human bifidobacteria have been well studied, most focus on one strain at a time, without considering the variety that coexist in the gut. My thesis focused on the ecological and evolutionary forces driving the assembly, coexistence, and functioning of bifidobacterial diversity. Using a multidisciplinary approach that encompasses ecological and evolutionary theory, genomics, and microbial metabolism, my objectives were to: 1) uncover the trait and evolutionary associations bifidobacteria have with their animal hosts (Chapter 1); 2) assess bacterial responses to dietary fiber consumption in the human gut (Chapter 2); and 3) identify the functional consequences of bifidobacteria diversity (Chapter 3).

To address objective 1, I used a comparative genomics approach to investigate the adaptation of bifidobacteria to their hosts. I analyzed all the bifidobacteria genomes available in The National Center for Biotechnology Information (NCBI) repository. I identified the hosts from which the bifidobacteria strains were isolated, performed a multilocus phylogenetic analysis, compared the genetic relatedness of the strains to different hosts, and tested the degree to which variation in traits can be attributed to their hosts. I found that different species of bifidobacteria colonized different animal hosts and that traits related to fiber degradation were associated with particular hosts.

To tackle objective 2, I conducted a meta-analysis that included dietary fiber interventions that have examined the human gut microbiome (n=21). By synthesizing, reanalyzing, and conducting an in-depth phylogenetic analysis, I found consistent bacterial responses to short-term increases in dietary fiber consumption in healthy humans. Specifically, I found that fiber interventions decreased bacterial diversity and explained an average of 1.5% of compositional variation. Moreover, I identified specific bacterial taxa that responded to dietary fiber in humans. One taxon that drastically increased in response to fiber consumption across interventions was bifidobacteria.

To address objective 3, I tested how the diversity and richness of bifidobacteria isolates influence their coexistence and functioning (i.e., fiber degradation) using laboratory experiments. To do this, I obtained bifidobacteria isolates from the Human Microbiome Project (HMP), and I selectively isolated new strains from fecal samples collected at the University of California, Irvine. I conducted microcosm experiments that vary the diversity of bifidobacteria and characterized the functioning of the bacterial communities using flow cytometry (to count bacterial cells), lactate assays (to measure metabolite concentration), and next-generation sequencing (to decipher the bacterial community’s composition). I found that the diversity of isolates persisted, such that up to 7 strains coexisted. Moreover, metabolite production (e.g., lactate) increased with increasing bifidobacteria diversity. However, this was not the case for biomass production.Focusing on the ecology and evolution of an important taxon like bifidobacteria within the diverse gut community will provide a deeper understanding on the community assembly mechanisms that bacteria use to colonize specific hosts.

Microbes are key players in global biogeochemical cycles. Despite their importance, many ecosystem models do not explicitly consider microbial communities and their functions. One reason for this is that we lack a quantitative understanding of the role that microbes play in biogeochemical processes, making their incorporation into models difficult. My dissertation takes a step towards establishing these links between microbial community composition and ecosystem function using two different approaches. The first approach was characterizing the patterns and drivers of a handful of traits associated with a key biogeochemical process, the nitrogen (N) cycle and then asking which taxa were associated with this trait. I tested this approach in one ecosystem and provided a blueprint of the nitrogen cycling potential of a grassland litter microbial community (Chapter 1). I then extended this work to characterize the global biogeography of microbial N cycling traits and investigated what environmental drivers might underlie these patterns (Chapter 2). Moving beyond patterns, understanding the processes driving the distribution of microbial communities presents a further challenge. Thus, the second approach taken in my dissertation was an experimental approach to investigate the local processes driving variation in bacterial community composition and functioning. More specifically, I focused on disentangling the effects of selection, drift, and dispersal on community assembly. First, I investigated how dispersal influences the assembly of this natural bacterial community using time series data from a field experiment (Chapter 3). I found that changing dispersal rate altered bacterial colonization rates and led to differences in the abundance, richness, evenness, and composition of communities. I then used another field experiment to quantify the role of stochastic processes in shaping microbial communities (Chapter 4). Here, I identified stochastic variation in bacterial community composition even after accounting for measurement error. Furthermore, stochastic variation in community composition translated into variation in functional parameters. Ultimately, the ability to accurately quantify stochastic processes is paramount to determining the predictability of community composition and functioning, whether focused on bacteria that degrade plant litter, microbes in the human gut, or patterns of global biodiversity.

Microbial communities are hard to study, yet their importance is hard to overstate. They inhabit every surface on Earth and are core participants in global biogeochemical cycling, but this is under threat due to anthropogenic climate change.One important microbiome is those communities that can be found decomposing leaf litter, the top layer of soil. This decomposition is critical for recycling nutrients back into the soil for the next generation of life. Here, I made use of microbial “cages” that permit water and nutrients to flow in and out while preventing microbial dispersal, allowing the study of microbes in situ. With the help of amplicon, metagenomic, and whole genome sequencing, and from the perspectives of ecology, evolution, and physiology, I dove into a single bacterial genus, Curtobacterium, to investigate the amount of ecologically important variation from closely related strains. I found evidence of variation between clades, with some strains surviving 10x better under desiccation than others. Further, variation exists between subclades, that might be missed using well-established methods of community analysis. I also investigated within a subclade, finding evidence that evolutionary processes operate during the timescale of ecological processes.

Global changes such as increased frequency of fire, drought, and nitrogen deposition, perturb microorganisms and the higher trophic life forms they support. Microorganisms play key roles in carbon and nutrient cycling, which are important to agriculture and ecosystem health. Although microorganisms are pivotal in an ecosystem's response to environmental changes, little is known about how abundant and diverse microbial communities adapt to such changes. The overarching aim of my thesis is to investigate how bacterial communities respond to global change and in particular, their ability to quickly adapt to environmental perturbations. I first investigated how microbial responses to global changes are influenced by interactions with plant communities using the Loma Ridge Global Change Experiment, a decade-long experiment that manipulates rainfall and nitrogen levels across two adjacent ecosystems (Chapter 1). My findings underscore the importance of plant–microbe interactions when considering the transferability of the results of global change experiments across ecosystems. Next, I investigated traits found on plasmids, a type of mobile genetic element (MGE) that can facilitate rapid evolution in bacteria. I asked what are the ecologically-relevant plasmid genes that may serve as reservoirs of environmental-adaptive traits in bacteria (Chapter 2). The findings of this chapter suggest that plasmid traits may contribute to host adaptation in environmental microbiomes. Lastly, I extended this work to a cosmopolitan soil taxon, Curtobacterium, an abundant genus of bacteria in southern California ecosystems. This taxon shows marked shifts in relative abundance in response to simulated drought and is amenable to culturing, providing a tractable system for investigating both genotypic and phenotypic characteristics of this organism. Previous experiments have shown Curtobacterium rapidly evolve via de novo mutations in response to environmental changes. I asked what MGE and associated traits are found in Curtobacterium, and determined whether MGE and traits showed any environment- versus clade- specific genomic signatures (Chapter 3). The findings of this chapter highlight the potential of traits found on plasmids to be mobilized within the bacterial communities where these Curtobacterium were isolated. Overall, my thesis work highlights the importance for considering the intersection of evolution and ecology in understanding how microbial communities adapt to environmental changes.

A central goal of global change biology is to predict the impact of environmental change on ecosystem processes. Currently, most global change models treat the local microbial community as a single, homogenously functioning entity, thereby assuming that the specific microbial composition is functionally irrelevant. However, microorganisms perform key transformations in ecosystems, and recent research demonstrates that microbial communities vary greatly across space and in response to environmental change. Therefore, parameters describing microbial communities may be key for improving predictions of how future global changes will impact ecosystem processes. For this reason, my dissertation research examined the effect of environmental changes on resident communities and determined how potential shifts in microbial community composition will impact litter decomposition rates. To accomplish this, I gathered litter samples from a chaparral ecosystem undergoing global change manipulations (elevated nitrogen availability or reduced precipitation), and characterized the microbial community using 454 high-throughput sequencing (Chapter 1). While microbial communities are much more variable through time, this research showed that microbial composition will likely shift in response to environmental change. I also examined the role of microbial community composition for a key ecosystem process, litter decomposition, and how that role changes under environmental perturbations. By isolating microbial taxa from the same ecosystem discussed above, I constructed artificial microbial communities with varying composition. I then conducted a laboratory experiment in which I subjected the communities to different global change manipulations and monitored decomposition rates and community composition (Chapter 2). Microbial composition had a main effect on leaf litter decomposition and also interacted with the environmental treatment, suggesting that future shifts in microbial communities will influence the magnitude in which environmental change affects ecosystem processes. Lastly, I investigated the functional and response traits of individual microbial taxa to better predict how microbial communities might respond to global change perturbations, and found that many functional traits displayed a phylogenetic pattern, but a taxa’s response to increased temperature did not (Chapter 3). Ultimately, this set of studies further justifies the need to incorporate microbial communities into models and begins to identify which parameters might be most relevant.