<p>Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.</p><p>With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.</p><p>In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them. </p><p>Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.</p> / Dissertation

Differences in microbial function via extracellular enzyme activity (EEA) were investigated to determine the potential effects of hydrology and plant-soil-microbe interactions in a young non-tidal freshwater riparian wetland. To study these relationships, three plots were established along a moisture gradient (Wet, Intermediate, Dry) within VCU Rice Center Within each main plot, five subplots were left undisturbed while another five were cleared of all above-ground plant biomass. Homogenized soil cores (top 10 cm) were analyzed for pH, redox, C:N, soil organic matter (SOM) content, saturation, and temperature. Microbial function was assessed using extracellular enzyme analysis. For most enzymes, a site difference was observed due to soil moisture content, which had an effect on soil pH, redox potential, and plant community composition. For most extracellular enzymes the presence of vegetation was associated with higher activity. It is important to note that reestablishing native hydrologic and vegetated conditions are paramount in achieving previous functionality.

[Truncated abstract] The principal aim of this thesis was to examine the response of the microbial community to the addition of small amounts (<50 μg C g-1 soil) of organic C substrates (‘trigger molecules’) to soil. This addition is comparative to indigenous soluble C concentrations for a range of soil types in Western Australia (typically measured between 20 and 55 μg C g-1 soil). Previously it has been reported that the application of trigger molecules to European soils has caused more CO2-C to be evolved (up to six fold) than was applied . . . Findings from this study indicated that there was an additional CO2 release (i.e. greater than the C added) on application of organic C substrates to some soil treatments. However, findings from this study indicate that the response of the microbial community to small additions of soluble C substrate is not consistent for all soil types and may vary due to greater availability of C, and supports the premise that microbial responses vary in a yet to be predicted manner between soil type and ecosystems. Differences in microbial response to the addition of soluble organic C are likely attributable to differences in soil attributes and environmental factors influencing both the diversity of microbes present and the frequency of food events. Theoretically, trigger molecules could also provide a possible control mechanism for microorganisms in arable farming systems. These mechanisms include stimulating either targeted pathogenic microorganisms that starve after depletion of a suitable substrate; or stimulating beneficial microorganisms to manipulate nutrient cycling, by targeting specific functional groups and altering mineralisation and immobilisation turnover rates.