The field of microbial ecology spans a diverse array of research topics, ranging from biogeography to biogeochemistry to community assembly. As a consequence of this broad focus, there are still many understudied components that require deeper understanding. Many dynamics related to microbial ecology have been examined in unstable systems that are prone to external perturbations. These studies are highly valuable in understanding community properties including resistance, resilience, and recovery, and have contributed significantly to our understanding of specific ecosystems. However, much of this work overlooks how communities develop over time in the absence of a strong disturbance, making it challenging to assess all aspects of microbial community stability. Beyond community assembly, the ecological drivers behind the broad diversity observed within domain Bacteria are currently not fully known. By examining the underlying genomic mechanisms responsible for developing bacterial diversity, we may better understand how specific functions are partitioned across phyla, enabling better predictions of ecosystem function. The work presented throughout this dissertation examines many of these qualities through a series of microbial ecology investigations performed in locations along an environmental stability gradient, as suggested by the degree of external disturbances.
Chapter 2 reports results collected from a semi-stable, well-connected, alluvial aquifer located near Rifle, CO. Groundwater microbial communities and geochemistry was tracked over a six-month period during which snowmelt-induced changes in local hydrology led to the intrusion of groundwater and dissolved oxygen into the vadose zone. This disturbance resulted in vertically and horizontally heterogeneous biogeochemical responses, which were related to shifts in redox chemistry. Within the microbial community, specific members demonstrated variable abundance associated with either increasing or decreasing oxygen concentrations. Reactive transport models supported empirical data suggesting that future predictions for future disturbances might be possible.
Chapter 3 discusses the results obtained dynamic hyporheic zone (HZ) located along the Colorado River during the same seasonal, snowmelt-induced river stage fluctuation. Vertically-resolved porewater samples were collected from the HZ during high, low, and base flow river stages, and used to measure biogeochemical shifts during associated hydrologic perturbations. Oxic river water was able to penetrate deepest into the HZ during peak flow while anoxic groundwater dominated the HZ during base flow. The 70 cm region of the riverbed that experienced these variable oxic-anoxic conditions exhibited seasonal fluctuations in redox chemistry. Relatedly, the microbial communities in this same region appeared to be distinct from those present in either river water or groundwater. Ecological modeling demonstrated that microbial communities experienced turnover related to the shifting redox landscape and experienced variable assembly processes.
Chapter 4 presents data collected from three relatively stable, unperturbed aquifers located throughout Ohio. Microbial and geochemical results collected every three months over two years revealed that although these systems did not experience significant external perturbation, the microbial communities assembled heterogeneously. In one aquifer, communities experienced significantly low turnover indicating homogenous selection. In others, however, results suggested that a combination of environmental filtering and homogenizing dispersal played significant role in microbial community assembly. Moreover, upon examining the degree of microbe-microbe relationships, greater phylogenetic turnover was observed between communities with larger differences in the degree of interconnectedness, as measured by cohesion.
Lastly, Chapter 5 examines the distribution, diversity, and functional potential of a recently described group of bacteria that phylogenetically place within the Candidate Phyla Radiation (CPR). Using shotgun metagenomic assembly and associated bioinformatics on 9 metagenomes from the same field sites, 71 CPR genomes were obtained, representing roughly 32 known phyla and 2 new putative phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. Given their previously implicated role in carbon degradation, the glycoside hydrolase profile of over 2000 previously sequenced CPR genomes plus these 71 CPR genomes were analyzed revealing patterns suggesting potential niche differentiation. The functional potential of the Parcubacteria superphylum was further expanded upon the discovery of a previously undescribed nitrite reductase, nirK, implicating these organisms in the transformation of nitrogen species.
Overall, this work expands our understanding of key community assembly processes and drivers of bacterial diversity across an environmental stability gradient. Null modeling methods revealed broad trends in microbial community assembly processes between the dynamic hyporheic zone and stable, poorly-connected aquifers. Intuitively, variable selection dominates dynamic environments whereas stable environments tend to experience either strong homogenous selection or moderate stochastic influences. Additionally, members of the CPR are distributed in each of these systems despite their diminutive genomes which feature limited biosynthetic and functional potential and variations in environmental stability. While the work presented in this dissertation explores understudied aspects of microbial ecology, it also highlights the necessity to expand research into more ecosystems across the stability gradient through the use of long-term, high resolution temporal datasets which incorporate microbial and geochemical data.