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The decomposition of plant litter is a critical biological function that aids in nutrient cycling and energy transfers within and between ecosystems. The primary decomposers of dead leaf material are bacteria and fungi, though there is no consensus as to which of these groups is dominant, nor is it known how the abundance and composition of these communities changes over time. The objectives of this study were to examine the relative contributions of bacterial and fungal populations to leaf organic matter (OM) decomposition and to consider the effect of moisture availability on the microbial community. The study was conducted across three habitats of differing moisture regimes: an upland terrestrial site, an emerging freshwater marsh, and an established freshwater swamp. Litterbags were constructed using two types of vegetation: a standardized substrate, maple leaves, and the site-specific vegetation, deployed in November 2007 following plant senescence, and retrieved after 0, 3, 6, 10, and 16 months of field incubation. The samples were then analyzed for decomposition as % OM remaining, total carbon and nitrogen content (C:N), dissolved organic carbon (DOC) release, microbial respiration via 14C heterotrophic uptake of acetate, and microbial community composition via terminal restriction fragment length polymorphism (T-RFLP) analysis. The results demonstrated that moisture regime is a significant factor in decomposition, with high decomposition at wetter sites. Vegetation type also impacted decomposition, as maple leaves were found to decay more similarly across sites, while the breakdown of site-specific vegetation varied more. These findings lack evidence to suggest one variable, moisture or vegetation time, as the driving factor of decomposition. Respiration rates varied greatly between sites and over time. Surprisingly, fungi were found to be a significant contributor to respiration at sites of high moisture, which suggests a need to better incorporated their activity in carbon budgets. Microbial communities were unique at each site and shifts were observed over time for both the bacterial and fungal populations. Changes in community structure were well correlated with changes in OM quality and quantity, though specific relationships varied by site. Future work determining functional groups and taxa of these microbial assemblages would provide a deeper knowledge of the role of these communities on decomposition processes. A better understanding of how differences in soil moisture impact decomposition rates will provide greater insight on the carbon sequestered or released from a habitat, which may be particularly important with global climate change. Although sites of high moisture exhibited accelerated decomposition, moisture alone may not be the driving factor. In turn, variables associated with high moisture, such as increased nutrients, should be further researched as they may actually be behind the increase in decomposition.

Bacterial communities are fundamental components of many processes occurring in aquatic ecosystems, since through microbial activities substantial amount of matter and energy is transferred from a pool of DOC to higher trophic levels. Previous studies highlighted the beneficial effects of diversity on ecosystem functioning, however studies on the resistance and resilience in microbial communities are scarce. Similarly, studies focusing on factors that might improve resistance or resilience of communities such as the influence of refuges are equally missing, although an understanding of the underlying mechanisms could be very useful in the field of conservation management. In this study, chemostat cultures were used to investigate the influence of a spatial and a temporal refuge on bacterioplankton communities’ resistance and resilience measured in terms of functioning and community composition after applying a salinity pulse disturbance. Respiration rate and substrate utilization were used to estimate bacterial functioning while community composition was determined by using T-RFLP. The perturbation was found to affect bacterial functioning and community composition. Moreover our findings indicate that the resistance and resilience measured in terms of bacterial functioning and community composition were significantly influenced by the provision of refuges.

Naturally occurring microbial communities from high-salt and/or high-temperature environments were collected from sites across the United States and Puerto Rico and screened for their efficacy in the MixAlco biofuel production platform. The MixAlco process, based on the carboxylate platform, is a sustainable and economically viable platform for converting lignocellulosic biomass to biofuels. Using a mixed culture of anaerobic organisms, lignocellulosic biomass is fermented into carboxylic acids, which are neutralized to their corresponding carboxylate salts. These salts can then be converted into a wide variety of chemical products and fuels (alcohols, gasoline, diesel, jet fuel). The central hypothesis is that microbial communities from relatively extreme environments, having evolved to withstand selection pressures similar to the conditions in the carboxylate platform, will exhibit high rates of biomass conversion. A total of 559 soil communities was screened as inocula in established laboratory-scale fermentations. We used pyrotag sequencing of 16S rRNA genes to characterize the bacterial components of the best-performing microbial communities. The best performing communities converted up to 3 times more biomass to acids than a standard marine community inoculum. The community analyses have allowed us to determine the extent to which the same functional types are favored during fermentation, at both laboratory and demonstration plant scales. In all cases, we observed a shift from the more diverse sediment community to post-fermentation communities with relatively low diversity dominated by organisms in the phylum Firmicutes, specifically Bacilli and Clostridia classes. Despite the fact that the inoculum sources were both geographically and ecologically diverse, all of the post-fermentation communities were more similar to each other in community structure than to the corresponding original inoculum community. In addition, studies of the sediments used as inocula revealed that environmental parameters, such as pH and water content, were significantly correlated with bacterial community composition. The wealth of data provided by current sequencing technologies allowed us to question whether communities with high process performances tend to achieve that performance with similar community structures.

The cpn60 gene is a DNA barcode for bacteria. Recently, the PCR primers that have been used extensively to amplify the cpn60 Universal Target (UT) region of bacteria were redesigned to improve their utility for fungal taxa. Additional novel primers were designed to amplify other regions of the cpn60 gene, specifically from fungal genomes. Design of the redesigned and novel primers was based on 61 nucleotide full-length cpn60 reference sequences available in 2012, including Ascomycota (51), Basidiomycota (5), Chytridiomycota (2), Glomeromycota (1), and Oomycota (2). The research described here investigated the utility of these primers for detecting and identifying fungal taxa and for profiling mixed communities of bacteria and fungi. The redesigned primers were used to discover cpn60 UT sequences for Ascomycota (1), Basidiomycota (2), and Chytridiomycota (1). The novel primers were used to discover new cpn60 sequence data for Ascomycota (3), Basidiomycota (1), and Zygomycota (1). To be adopted for use in studies of microbial communities that are predominantly bacterial, the redesigned cpn60 UT primers must perform at least as well as the original primers for bacterial profiling. Bacterial profiles, created using the original and redesigned primers and two DNA template samples created by pooling DNA extracts from vaginal swabs from individual women, were compared. These included comparisons of diversity indices, rarefaction curve analysis and Operational Taxonomic Unit abundances. Diversity indices and rarefaction curve analysis for bacterial profiles with original and redesigned primers were similar. OTU abundance estimates with the original and redesigned primers were compared at higher and lower taxonomic levels. The overall patterns produced were similar. For one template only, the phylum Bacteroidetes had a greater apparent abundance with the original primers than with the redesigned primers. The greater apparent abundance of Bacteroidetes taxa was balanced by a lesser apparent abundance of taxa that were not assigned to a phylum. These differences may reflect differences in the performance of the two primer sets. At lower taxonomic level, most OTU were represented with apparently equal abundances with redesigned and original primers in same template. Very few OTU were represented with different proportional abundances with redesigned and original primers. Different OTU having same reference cpn60 UT sequence as best hit were sometimes represented by different proportional abundance with same primer in same template that made the analysis difficult. On the whole, the redesigned cpn60 UT primers behaved at least as good as the original cpn60 UT primers. The overall results showed that the redesigned and novel primers used in this study had substantial utility for the identification of fungal samples and mixed microbial communities.

Polymicrobial communities often show complex patterns of metabolic and ecological interactions, yet our understanding of how the properties of communities emerge from the metabolic rules of species interactions is still limited. A central feature of metabolic interactions within microbial communities is ‘cross-feeding’, where one species or lineage consumes the metabolic by-products of another. Cross-feeding bacteria excrete and consume a wide range of metabolites and this sets the stage for diverse intra- and inter-specific metabolic interactions. In this thesis, I use ecological and evolutionary theory to address a number of critical questions posed by cross-feeding bacteria, with a particular focus on the role played by microbial metabolism in driving the emergence and dynamics of microbial interactions. First, I explore the conditions that favour the emergence and maintenance of cooperative cross-feeding and show that the evolutionary outcome depends strongly on the shape of the trade-off curves between the costs and benefits of cooperation. Second, I investigate the origins of cross-feeding interactions via single lineage diversification and derive new predictions on the physiological mechanisms that may explain the stable coexistence of a cross-feeding polymorphism that evolved from a single clone. Third, I investigate what are the ecological consequences of cross-feeding metabolic interactions and demonstrate theoretically that a simple mechanism of trade can generate a diverse array of ecological relationships. Furthermore, I show the importance of the metabolic by-product properties in determining the ecological outcome. Fourth, I investigate how metabolic constraints of individual species shape the emergent functional and structural relationships among species. I show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Furthermore, I show that these emergent community properties are driven by demographic feedbacks. In general, these findings support the idea that bridging microbial ecology and metabolism is a critical step toward a better understanding of the factors governing the emergence and dynamics of polymicrobial interactions.

Soil salinity is a widespread problem that affects crop productivity. We expect that saline soils also have altered microbial community structure, soil food webs and related soil properties. To test this, we sampled field soils across four farms in eastern North Dakota that host salinity gradients. We evaluated microbial biomass carbon, phospholipid fatty acid analysis and nematode counts in moderately saline and low saline soils. Additionally, we measured soil properties that represent potential food sources and habitat characteristics that influence microbial communities. We found higher microbial group abundance in moderately saline soils than in the lower saline soils. In contrast, we found lower nematode abundances in the moderately saline soils. We also observed increased labile carbon, nitrogen, phosphorus, and water content in the moderately saline soils. Based on our results, saline soils appear to have unique soil biological characteristics, which have implications for overall soil function along salinity gradients.