Microbial Community Structure And Ecosystem Function In A Changing World

Understanding the effects climate change will have on the structure and function of global ecosystems is a pressing ecological and social issue. Global change driven changes in atmospheric warming and precipitation régimes have begun to alter the distribution of plants and animals in, as well as the function of, ecosystems. Using two large-scale climate change manipulations, I assessed the effect of changing precipitation and temperature regimes on soil microbial community structure and function. Soil microbial communities regulate decomposition and nutrient cycling rates in ecosystems, thus understanding their response to climatic changes will enable scientists to better predict carbon feedbacks to the atmosphere as well as functional shifts within ecosystems. My first two chapters took advantage of a large-scale precipitation manipulation in a semi-arid woodland. My first chapter aimed to understand how changing precipitation amounts altered the structure and abundance of soil bacteria and fungi; while my second chapter measured how changing precipitation altered soil nitrogen cycling. Overall, I found that soil microbial community composition and function were responsive to changes in precipitation, but these responses were contingent upon seasonal variability in precipitation and the aboveground plant community. My final experiment examined how changing temperature altered soil microbial community structure and function in two temperate forests. Using a large scale warming experiment at two locations, I examined how changes in temperature altered microbial composition, abundance, potential enzyme activity, and decomposition. I found that the effects of warming were contingent upon location; microbial community composition responded to alterations in soil temperature and soil moisture at the warmer site, but not at the cooler site. Unexpectedly, the change in microbial community composition did not result in changes in the rate of decomposition. I conclude that the soil is relatively buffered from atmospheric warming thus changes in microbial community structure and function may take longer than a few years to develop. Taken together, my research demonstrates that understanding the effects of climate change on microbial community structure and function is complex and contingent upon the background abiotic and biotic variability within an ecosystem

The effects of insects, nutrients, and plant invasion on community structure and function above- and belowground

Soil nutrient availability, invasive plants, and insect presence can directly alter ecosystem structure and function, but less is known about how these factors may interact. In this 6-year study in an old-field ecosystem, we manipulated insect abundance (reduced and control), the propagule pressure of an invasive nitrogen-fixing plant (propagules added and control), and soil nutrient availability (nitrogen added, nitrogen reduced and control) in a fully crossed, completely randomized plot design. We found that nutrient amendment and, occasionally, insect abundance interacted with the propagule pressure of an invasive plant to alter above-and belowground structure and function at our site. Not surprisingly, nutrient amendment had a direct effect on aboveground biomass and soil nutrient mineralization. The introduction of invasive nitrogen-fixing plant propagules interacted with nutrient amendment and insect presence to alter soil bacterial abundance and the activity of the microbial community. While the larger-scale, longer-term bulk measurements such as biomass production and nutrient mineralization responded to the direct effects of our treatments, the shorter-term and dynamic microbial communities tended to respond to interactions among our treatments. Our results indicate that soil nutrients, invasive plants, and insect herbivores determine both above-and belowground responses, but whether such effects are independent versus interdependent varies with scale

The effects of insects, nutrients, and plant invasion on community structure and function above- and belowground

Soil nutrient availability, invasive plants, and insect presence can directly alter ecosystem structure and function, but less is known about how these factors may interact. In this 6-year study in an old-field ecosystem, we manipulated insect abundance (reduced and control), the propagule pressure of an invasive nitrogen-fixing plant (propagules added and control), and soil nutrient availability (nitrogen added, nitrogen reduced and control) in a fully crossed, completely randomized plot design. We found that nutrient amendment and, occasionally, insect abundance interacted with the propagule pressure of an invasive plant to alter above- and belowground structure and function at our site. Not surprisingly, nutrient amendment had a direct effect on aboveground biomass and soil nutrient mineralization. The introduction of invasive nitrogen-fixing plant propagules interacted with nutrient amendment and insect presence to alter soil bacterial abundance and the activity of the microbial community. While the larger-scale, longer-term bulk measurements such as biomass production and nutrient mineralization responded to the direct effects of our treatments, the shorter-term and dynamic microbial communities tended to respond to interactions among our treatments. Our results indicate that soil nutrients, invasive plants, and insect herbivores determine both above- and belowground responses, but whether such effects are independent versus interdependent varies with scale

Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer

Epithelial ovarian cancer (OC) is the most deadly cancer of the female reproductive system. To date, there is no effective screening method for early detection of OC and current diagnostic armamentarium may include sonographic grading of the tumor and analyzing serum levels of tumor markers, Cancer Antigen 125 (CA-125) and Human epididymis protein 4 (HE4). Microorganisms (bacterial, archaeal, and fungal cells) residing in mucosal tissues including the gastrointestinal and urogenital tracts can be altered by different disease states, and these shifts in microbial dynamics may help to diagnose disease states. We hypothesized that the peritoneal microbial environment was altered in patients with OC and that inclusion of selected peritoneal microbial features with current clinical features into prediction analyses will improve detection accuracy of patients with OC. Blood and peritoneal fluid were collected from consented patients that had sonography confirmed adnexal masses and were being seen at SIU School of Medicine Simmons Cancer Institute. Blood was processed and serum HE4 and CA-125 were measured. Peritoneal fluid was collected at the time of surgery and processed for Next Generation Sequencing (NGS) using 16S V4 exon bacterial primers and bioinformatics analyses. We found that patients with OC had a unique peritoneal microbial profile compared to patients with a benign mass. Using ensemble modeling and machine learning pathways, we identified 18 microbial features that were highly specific to OC pathology. Prediction analyses confirmed that inclusion of microbial features with serum tumor marker levels and control features (patient age and BMI) improved diagnostic accuracy compared to currently used models. We conclude that OC pathogenesis alters the peritoneal microbial environment and that these unique microbial features are important for accurate diagnosis of OC. Our study warrants further analyses of the importance of microbial features in regards to oncological diagnostics and possible prognostic and interventional medicine.Ope

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation

Soil microbiome responses to short-term nitrogen (N) inputs remain uncertain when compared with previous research that has focused on long-term fertilization responses. Here, we examined soil bacterial/archaeal and fungal communities pre- and post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0–5 and 5–15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions for assessment of microbial community composition. Baseline assessments prior to fertilization revealed no significant pre-existing divergence in either bacterial/archaeal or fungal communities across plots. The one-time N fertilizations increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12–22% of the variation as calculated from the Sq. root of PERMANOVA tests for bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. These results suggest that short-term effects of N fertilization are significant but subtle, and other sources of variation will need to be carefully accounted for study designs including multiple intra-annual sampling dates, rather than one-time “snapshot” analyses that are common in the literature. Continued analyses of these trends over time with fertilization and management are needed to understand how these effects may persist or change over time

Non-Additive Effects of Genotypic Diversity Increase Floral Abundance and Abundance of Floral Visitors

Background: In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention. Methodology/Principal Findings: Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot) of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1) plant genotype explained 45 % and 92 % of the variation in flower visitor abundance in 2007 and 2008, respectively; and 2) plant genotypic diversity had a positive and non-additive effect on floral abundance and the abundance of flower visitors, as plots established with multiple genotypes produced 25 % more flowers and received 45 % more flower visits than would be expected under an additive model. Conclusions/Significance: These results provide evidence that declines in genotypic diversity may be an important but little considered factor for understanding plant-pollinator dynamics, with implications for the global decline in pollinators due t

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization

Data from: The effects of insects, nutrients, and plant invasion on community structure and function above- and belowground

Soil nutrient availability, invasive plants, and insect presence can directly alter ecosystem structure and function, but less is known about how these factors may interact. In this 6-year study in an old-field ecosystem, we manipulated insect abundance (reduced and control), the propagule pressure of an invasive nitrogen-fixing plant (propagules added and control), and soil nutrient availability (nitrogen added, nitrogen reduced and control) in a fully crossed, completely randomized plot design. We found that nutrient amendment and, occasionally, insect abundance interacted with the propagule pressure of an invasive plant to alter above- and belowground structure and function at our site. Not surprisingly, nutrient amendment had a direct effect on aboveground biomass and soil nutrient mineralization. The introduction of invasive nitrogen-fixing plant propagules interacted with nutrient amendment and insect presence to alter soil bacterial abundance and the activity of the microbial community. While the larger-scale, longer-term bulk measurements such as biomass production and nutrient mineralization responded to the direct effects of our treatments, the shorter-term and dynamic microbial communities tended to respond to interactions among our treatments. Our results indicate that soil nutrients, invasive plants, and insect herbivores determine both above- and belowground responses, but whether such effects are independent versus interdependent varies with scale

Appendix C. Results from ANOVA testing the effects of climate-change treatments on extracellular enzyme activities in plant community soils and in plant-specific soils.

Results from ANOVA testing the effects of climate-change treatments on extracellular enzyme activities in plant community soils and in plant-specific soils