Fitness, the competitive advantage of an organism or gene, is the basis for adaptation and the emergence of complexity in biology. Competitive advantage is contextual, as it is affected by environmental pressures and ecological interactions. To enable experiments with complex environmental dynamics, we developed eVOLVER, a novel platform for scalable programmable continuous culture. In this thesis, we apply eVOLVER to interrogate how competitive outcomes between strains change according to environmental conditions. Using soil microbe communities as a model ecological system, we tuned dilution rate and frequency across 112 cultures in eVOLVER and observed replicable changes in composition and diversity. Our experimental results challenge intuition about the relationship between diversity and disturbance. In collaborative work, we compared different models of competitive growth in simulations. A Monod growth model outperforms Lotka-Volterra and linear consumer resource models at predicting the effect of varying dilution profiles on microbial diversity. We hypothesize that trade-offs in growth rate and nutritional requirements (r/K) create distinct niches which permit coexistence at certain mortality rates, but collapse under others. These findings suggest a mechanism that potentially affects diversity-disturbance relationships, and confirm that temporal fluctuations can promote diversity. In separate studies, we apply these methods and concepts to 1) study selection on a genome-scale library in yeast under conditions of fluctuating temperature stress in eVOLVER and 2) evaluate the persistence of engineered microbial spores relative to native strains in different “real-world” environments (e.g. soil) and perturbations. Broadly, this dissertation demonstrates that the combination of next-generation sequencing and scalable programmable culture technologies finally enables the types of experiments needed to test decades of theoretical work in ecology and evolution. / 2021-05-18T00:00:00Z

Ensyeh Sarikhani Soil microbial communities in agroecosystems and natural habitats contributing to resistance and resilience of the soil environment. Summary The control of common scab of potatoes (CS) includes resistant varieties (cultivars), precise fertilization, increase of soil moisture, and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. A monitoring study was done in 32 sites to evaluate the relation between CS and biological/chemical soil parameters. Correlations were observed between scab severity and content of nutrients such as Fe, N, and Ca in soil and periderm, and between disease severity and abundance of actinobacteria and total bacteria, together with the pathogenicity determinant, txtB gene (biosynthetic gene of thaxtomin) in both soil and periderm of potatoes. The findings led to novel conclusions, which can help to understand relationships applicable in scab control. Peat and DTPA chelated iron were supplemented to pots filled with soil conducive for CS in order to determine the effects of soil organic matter, iron and pH on CS development. The results were compared with data obtained for a suppressive soil from a nearby field with naturally low CS severity. Both peat and iron supplements decreased CS and the combination...

Pharmaceuticals are micropollutants, that enter the environment mainly through Wastewater Treatment Plants (WWTPs). In this work microbial community has been studied in sediments of a stream, which is located near a WWTP. This sediment is contaminated with pharmaceuticals. The subject of this thesis was to determine the presence of pharmaceuticals and microbial community in this study site and to point out possible relationships between these factors. Twelve pharmaceuticals were identified at concentrations reaching levels of ng/g. The concentrations of the compounds form a gradient that decreases with the distance from WWTP. Microbial biomass was estimated using the analysis of phospholipid fatty acids and microbial community was described using next-generation DNA sequencing. The analysis of phospholipid fatty acids pointed out, that with the increasing distance from WWTP the amount of microbial biomass decreases. DNA sequencing revealed large microbial diversity in the studied sediment. For evaluation of the relationship between the microbial community and pharmaceuticals in the stream sediment, Principal Component Analysis (PCA) was used. The result of PCA showed, that in the stream sediment (depth 10-30 cm), Betaproteobacteria negatively correlated with triclosan and Clostridia negatively...

<p>Little is known about how the leaf bacterial community is affected by the seed microbiota at different stages of plant development. The bacterial populations of spinach seed and leaves after germination were compared using DGGE, to assess bacterial community richness, and real-time PCR to compare the abundance of select phyla (total bacteria, <i>Actinobacteria, Bacteroidetes, Firmicutes, α-Proteobacteria and β- Proteobacteria</i>). To determine the effect of environment, the plants were grown in the field and growth chambers. Vertical transmission of bacterial community members was evident; the developmental stage of the plant affected the richness and abundance of select bacterial phyla. The bacterial richness of plants grown in the two environments was not affected. However, overall numbers of bacteria increased in field grown samples in comparison to those produced in growth chambers during development. A statistically significant interaction was seen between growth stage and environment with each of the selected phyla. Populations on cotyledons were smaller than mature leaves, but were not significantly different than the 3-4 leaf stage plants. The culturable populations of bacteria on seeds (~5 log CFU/g) were significantly smaller than determined using real time PCR (~7 log copies). Of these bacteria cultured from spinach seeds, isolates belonging to the genera <i>Pantoea</i> were found to inhibit growth of <i>E. coli</i> O157:H7 <i>in vitro</i>. This study highlights the importance of vertical transmission on the bacterial community of plants and suggests the importance of developing strategies to influence these communities on seed to control human and plant pathogens on the leaf surface.</p> / Master of Science

Pyrogenic ecosystems are maintained by fires which vary in frequency, seasonality, and intensity. Florida oak-saw palmetto scrub ecosystem is characterized by fires occurring at intervals of 10-20 years. Diverse factors as private land acquisition and development has created a patchy distribution of scrub ecosystems and also interrupted the natural fire cycle. The effects of fire over plant regeneration and fauna habitat utilization of the scrub have been well characterized in previous research. In the present paper the objective is to characterize the short- and long-term fire effects on the soil microbial community. Fire effects were studied in a chronosequence, comprising a recently burned scrub during a winter-prescribed fire to scrub where fire did not occur for 40 years. The number of culturable cells was reduced by two orders of magnitude by indirect fire effects and environmental factors, principally hydric stress. However, the duration of fire effects was very short since the microbial community returned to pre-fire numbers and activity by day 47 after fire. Microbial community activity was distinctively related to inoculum density in the soil and litter samples. Soil and litter microbial communities showed differences in metabolic activity. There was no difference in substrate utilization pattern, but there was significant seasonal variation related to the decrease in water content during the month of May. Substrate utilization by litter microbial communities was higher during the month of January compared to soil microbial communities and this relationship was inversed during the month of May probably associated to the more stringent conditions, low water availability, on the litter layer. Seasonal effects outweighed fire effects in this study as this environmental constraint determined the microbial community structure and activity.

Microbial communities play critical roles in biogeochemical cycles of aquatic and terrestrial ecosystems, but studies of soil microbial communities have been limited by the diversity and complexity found in most ecosystems. Here we report on work investigating the functional diversity of microbial mat and underlying soil communities in the McMurdo Dry Valleys of Antarctica across a gradient of phosphorus availability on glacial tills of distinct age and mineral composition in Taylor Valley, Antarctica. Microbial mat and soil DNA were extracted and sequenced on an Illumina NextSeq500 in a 150 bp paired end format. Raw sequences were uploaded to the MG-RAST server for processing and annotation. Community taxonomic and functional annotation were determined using the RefSeq and SEED Subsystem databases, respectively. The results revealed significant variation in microbial mat community taxonomic composition between the two tills, strongly associated with visual assessment of mat morphology, e.g., "black" and "orange" mats, and soil N:P ratios. The underlying soil microbial communities did not exhibit significant differences in diversity between the two tills, but community composition varied significantly across gradients of soil chemistry, particularly extractable-phosphate content even within tills. The relative abundance of biogeochemistry-relevant pathways determined from the SEED database varied amongst soil microbial communities between the two tills. For example, microbial mat communities exhibited significant variation in the relative abundance of key nitrogen and phosphorus metabolism associated genes strongly associated with the underlying soil N:P. These results suggest that spatial variation in geochemistry influences the distribution and activity of microbial mats, but that the microbial mats themselves also exert a significant homogenizing effect on the underlying soil communities and some of the key biogeochemical processes they facilitate. / Master of Science / Microbial communities play critical roles in the processes of aquatic and terrestrial ecosystems. Still, studies of soil microbial communities have been limited by the complex nature of the ecosystems we study. This study examined the diversity of microbial communities in the McMurdo Dry Valleys of Antarctica, specifically looking at how different levels of phosphorus availability in the soil affected microbial function. We used DNA sequencing and databases to determine the taxonomic and functional makeup of these communities. We found that while the microbial mat communities varied significantly based on soil chemistry and appearance, the underlying soil microbial communities did not. We also found evidence suggesting that the microbial mats played a role in regulating some of the key ecosystem processes in the soil. Overall, this study sheds light on how microbial communities are impacted by their environment and how they, in turn, impact their surroundings.

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