A major objective of biodiversity-ecosystem functioning (BDEF) research is to determine the consequences of species loss, caused both naturally and anthropogenically, on the functioning of ecosystems. The impact of plant species loss on the soil microbial community has not received much attention even though soil microbes influence many important ecosystem functions such as decomposition and nutrient cycling. The objective of this research was to investigate how the functional group composition of the aboveground plant community influenced the belowground microbial community. Plant functional groups (graminoids, legumes and non-leguminous forbs) were removed from a northern grassland system in the Yukon Territory, Canada. One metre square plots had one of the three functional groups removed or left intact as a control and this was crossed with a fertilizer treatment and a fungicide treatment that targeted mycorrhizal fungi. After five seasons (2003-07) of implementing treatments the soil microbial community was analyzed using substrate-induced respiration (SIR, a measure of metabolic diversity) and phospholipid fatty acid analysis (PLFA, a measure of community composition). Plant functional group removal had almost no effect on the soil microbial community. The only response detected was an increase in stress (indicated by the PLFA stress ratio of cy19:0 to 18:1ω7c) which occurred when legumes were removed and fertilizer was not added, indicating that legumes had a positive effect on the nutrient status of microbes. Likewise, soil properties (total carbon, pH, moisture and nutrients) showed limited response to plant removals. Fertilization decreased the metabolic diversity of the soil microbial community. We detected no soil microbial or plant biomass response to the fungicide indicating that mycorrhizae had little influence in this system. Based on the low-productivity of the grassland, and the lack of response in both the soil properties and the microbial community, we hypothesize that the main determinants of the microbial community may be litter input. When litter decomposition rates are slow, such as in this northern system, five growing seasons may not be sufficient to detect the impact of a changing plant community on the soil microbes.

A major objective of biodiversity-ecosystem functioning (BDEF) research is to determine the consequences of species loss, caused both naturally and anthropogenically, on the functioning of ecosystems. The impact of plant species loss on the soil microbial community has not received much attention even though soil microbes influence many important ecosystem functions such as decomposition and nutrient cycling. The objective of this research was to investigate how the functional group composition of the aboveground plant community influenced the belowground microbial community. Plant functional groups (graminoids, legumes and non-leguminous forbs) were removed from a northern grassland system in the Yukon Territory, Canada. One metre square plots had one of the three functional groups removed or left intact as a control and this was crossed with a fertilizer treatment and a fungicide treatment that targeted mycorrhizal fungi. After five seasons (2003-07) of implementing treatments the soil microbial community was analyzed using substrate-induced respiration (SIR, a measure of metabolic diversity) and phospholipid fatty acid analysis (PLFA, a measure of community composition). Plant functional group removal had almost no effect on the soil microbial community. The only response detected was an increase in stress (indicated by the PLFA stress ratio of cy19:0 to 18:1ω7c) which occurred when legumes were removed and fertilizer was not added, indicating that legumes had a positive effect on the nutrient status of microbes. Likewise, soil properties (total carbon, pH, moisture and nutrients) showed limited response to plant removals. Fertilization decreased the metabolic diversity of the soil microbial community. We detected no soil microbial or plant biomass response to the fungicide indicating that mycorrhizae had little influence in this system. Based on the low-productivity of the grassland, and the lack of response in both the soil properties and the microbial community, we hypothesize that the main determinants of the microbial community may be litter input. When litter decomposition rates are slow, such as in this northern system, five growing seasons may not be sufficient to detect the impact of a changing plant community on the soil microbes.

A major objective of biodiversity-ecosystem functioning (BDEF) research is to determine the consequences of species loss, caused both naturally and anthropogenically, on the functioning of ecosystems. The impact of plant species loss on the soil microbial community has not received much attention even though soil microbes influence many important ecosystem functions such as decomposition and nutrient cycling. The objective of this research was to investigate how the functional group composition of the aboveground plant community influenced the belowground microbial community. Plant functional groups (graminoids, legumes and non-leguminous forbs) were removed from a northern grassland system in the Yukon Territory, Canada. One metre square plots had one of the three functional groups removed or left intact as a control and this was crossed with a fertilizer treatment and a fungicide treatment that targeted mycorrhizal fungi. After five seasons (2003-07) of implementing treatments the soil microbial community was analyzed using substrate-induced respiration (SIR, a measure of metabolic diversity) and phospholipid fatty acid analysis (PLFA, a measure of community composition). Plant functional group removal had almost no effect on the soil microbial community. The only response detected was an increase in stress (indicated by the PLFA stress ratio of cy19:0 to 18:1ω7c) which occurred when legumes were removed and fertilizer was not added, indicating that legumes had a positive effect on the nutrient status of microbes. Likewise, soil properties (total carbon, pH, moisture and nutrients) showed limited response to plant removals. Fertilization decreased the metabolic diversity of the soil microbial community. We detected no soil microbial or plant biomass response to the fungicide indicating that mycorrhizae had little influence in this system. Based on the low-productivity of the grassland, and the lack of response in both the soil properties and the microbial community, we hypothesize that the main determinants of the microbial community may be litter input. When litter decomposition rates are slow, such as in this northern system, five growing seasons may not be sufficient to detect the impact of a changing plant community on the soil microbes. / Science, Faculty of / Botany, Department of / Graduate

Thesis advisor: Heather Craig Olins / Microbes play a critical role in the Earth’s ecosystems, and freshwater microbial communities are underappreciated players in biogeochemical cycles. Vernal pools are ecologically important habitats that are particularly sensitive to global warming. Microbial communities in vernal pools and other freshwater wetlands are both critical to supporting life on Earth as well as incredibly vulnerable to climate change. This thesis describes for the first time microbial community composition in freshwater wetlands in Newton, Massachusetts. Beta diversity analysis reveals that sites host distinct microbial communities, something not always seen at these spatial scales. Sediment samples from the Bare Pond vernal pool were dominated by Acidobacteria, Actinobacteria, Alphaproteobacteria, and Chloroflexi. Analysis of surface vs. subsurface sediment samples reveal taxonomic patterns that cross multiple sites. These findings are a first step towards better understanding ecologically important microbial activity in these local sites, and freshwater wetlands more broadly. / Thesis (BS) — Boston College, 2020. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Departmental Honors. / Discipline: Biology.

Acid Mine Drainage (AMD) is characterized by high metal concentrations and an extremely low pH, primarily generated by the microbial oxidation of iron sulfides from mine tailings. Research on the microbial AMD community has largely focused on Bacteria, while little information is known about the Archaeal and Eukaryote members or the seasonal patterns within the communities. Here I examined the Bacterial, Archaeal, and eukaryotic AMD seasonal microbial community, using direct sequencing techniques on AMD samples from the Copper Cliff Tailings AMD site in Sudbury, Ontario, Canada. I found large variation in the community profile and species composition between sampling times of both the Bacterial and Eukaryote communities, suggesting a dynamic community, both between and within seasons. Bacterial diversity was highest during the winter, with Acidithiobacillus dominating, while during the summer, Acidiphilium was the dominant genus. The winter Eukaryote community was dominated by classes of algae and fungi, while the majority of summer sequencing could not be classified to the class level. Few reads were obtained for the Archaeal domain, with low and similar biodiversity between seasons. Overall, the AMD community variation and abundance were found to largely correlate with drainage water and seasonal temperature.

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.

The human microbiome, the complex and dynamic ecosystem that populates our body, performs essential functions such as aiding digestion and protecting us from harmful pathogens. An increasing number of diseases are found to be associated with a shift of balance - or dysbiosis - of the microbiome. However, we still know little about this delicate balance and how it depends on different microbial functions. In this thesis project, I used metagenomic sequencing data to study the variability of microbes and their functions in different areas of the human body. First, in an attempt to characterize the dysbiosis associated with periodontitis, I examined the microbial community of the oral cavity in presence and absence of this chronic inflammatory disease. Specifically, I catalogued the phylogenetic signatures composed of tetramer nucleotide frequencies and observed that the disease state occupies a much narrower region than the healthy one. This result suggests that upon onset of the disease, through host cell invasion, pathogenic bacteria may find a more consistent environment for their parasitic lifestyle. Motivated by these findings, I sought further evidence of an environment-specific use of metabolic functions in the oral and gut communities. Rather than focusing on the abundance of individual metabolic functions, I evaluated their diversity, i.e., the extent to which these functions are performed by different classes of organisms. My hypothesis was that such diversity may confer increased robustness to taxonomic variability. Using metagenomic sequencing data and NCBI's Protein Clusters database, I characterized the multiplicity of gene families associated with a given metabolic function. I found that different human body sites display different degrees of metabolic functional diversity, as assessed by Shannon entropy. For some well-studied gene functions, such as those involved in glycolytic pathways, I found entropy signatures consistent with the known degree of oxygen availability of different environmental niches. Conversely, in an unsupervised analysis, I identified functions with nontrivial entropy signatures. These results pave the way for a new way to inspect human microbiome activity, and could help understand its functional resilience and suggest ways to shift its balance towards healthy configurations.

The spotted bird grasshopper, Schistocerca lineata Scudder (Orthoptera: Acrididae), is a widely distributed species found throughout most of the continental United States and southern Canada. This species is known to be highly variable in morphology, with many distinct ecotypes across its native range. These ecotypes display high levels of association with type-specific host plants. Understanding the evolutionary relationships among different ecotypes is crucial groundwork for studying the process of ecological differentiation. I examine four ecotypes from morphological and phylogeographic perspectives, and look for evidence of distinct evolutionary lineages within the species. I also begin to explore the potential role of the microbial community of these grasshoppers in ecological divergence by using 454 pyrosequencing to see if the microbial community structure reflects the ecology of the grasshoppers. I find support for a distinct aposematic lineage when approaching the data from a phylogeographic perspective and also find that this ecotype tends to harbor a unique bacterial community, different from that of a single other ecotype.

The effects of an organic biocide (CTN) with and without coded antioxidant (BHT) on microbial communities in SYP were assessed using terminal restriction fragment length polymorphism (T-RFLP) analyses in both field and accelerated decay laboratory studies. Ammoniacal copper quaternary (ACQ-C) was used as a positive control in the field study component, but not in the laboratory test. Field stakes were treated with 0.25 and 0.37% ammoniacal copper quat (ACQ-C), CTN (0.1 and 0.25%), CTN (0.1 and 0.25%) with 2% BHT added, 2% BHT alone, and controls were left untreated. In the field studies, preservative treatment slowed the initial colonization of wood by fungi. Higher species richness and diversity were found in non-biocidal treatments (BHT and untreated controls). Fungal communities in treated wood were different based on their species composition, but eventually became more similar to untreated controls. Preservative treatment increased richness and diversity of basidiomycete fungi, but overall presence of basidiomycetes was low compared to other fungi. Preservatives did not change the species composition of basidiomycetes compared to untreated controls. Preservative treatment initially increased bacterial richness and diversity, but over time these trends diminished to levels consistent with untreated controls. Preservatives changed the species composition of colonizing bacteria so that treated and untreated communities remained different over 15 months of soil exposure. Bacterial diversity was negatively correlated with CTN depletion at the lowest rate. In the accelerated decay laboratory test, the effects of CTN and/or BHT on bacterial, fungal, and basidiomycete communities in composted and uncomposted soil were evaluated over a 12 month period. Composted soil had less fluctuation in changing microbial diversity due to more constant moisture. The consensus of the analyses of the bacterial, fungal, and basidiomycete communities indicate that wood preservatives increased microbial species richness and diversity. Preservative treatment increased species turnover that decreased over time. Eventually, microbial communities approached a stable community structure consistent with untreated controls. Preservatives were completely degraded after 30 days exposure; however, definite changes in bacterial and fungal richness, diversity, and species composition were found. Basidiomycetes again represented the smallest portion of the microbial community involved in the overall decay process.

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