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Author ORCID Identifier

https://orcid.org/0000-0002-9108-5083

Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Organismic and Evolutionary Biology

Year Degree Awarded

2019

Month Degree Awarded

September

First Advisor

Laura A Katz

Second Advisor

Tanja Woyke

Third Advisor

Courtney Babbitt

Fourth Advisor

Kristina Stinson

Subject Categories

Terrestrial and Aquatic Ecology

Abstract

Soil is considered one of the most diverse ecosystems on Earth, harboring diversity of organisms across the three domains of life. It is spatially and chemically heterogeneous: properties that intertwine in a complex matrix to support organismal diversity and function across different scales. Soil microorganisms both respond to and drive changes in ecosystems through metabolic activities. A single gram of soil is teeming with millions of cells comprised of thousands of species. Much of this diversity remains uncharacterized due to technical and methodological challenges faced by soil ecologists. Due to the complex physicochemical properties of soil and cross-feeding interactions between organisms, it is difficult to culture microorganisms in isolation. The immense biological diversity of soils also reduces bioinformatic genome assembly efficiency, therefore obscuring the scope of diversity. As one of Earth's main reserviors of stored carbon, containing roughly one-third of carbon globally, terrestrial ecosystems may serve as a carbon source under future climate scenarios and drive further climate change. Despite challenges associated with the study of soil microorganisms, it remains critical to discover and describe diversity of microbial communities in soils if we are to understand resilience of our ecosystems to climate change.

Surveys of microbial diversity and function in soil have been conducted using amplicon sequencing, metagenomics, and metatranscriptomics, however a large knowledge gap persists in the characterization of diversity and ecological niches of elusive microorganisms. These are organisms that are typically recalcitrant to laboratory culture, and may appear in relatively low abundance in soil communities or exhibit a high degree of population microheterogeneity, thereby resulting in poor representation in genome assemblies. The focus of my dissertation research is the application of complementary genomic techniques in order to uncover more of the previously unknown microbial diversity contained in forest soils, and link this diversity to higher-level ecosystem function. Much of what is known about soil diversity has been contributed through cultivation-independent investigations, however diversity estimates indicate that we are only beginning to scratch the surface of bacterial, archaeal, and viral diversity in forest soils. We are therefore vastly underestimating the roles these organisms play in biogeochemical processes, such as the release of CO2 to the atmosphere through respiration. However, the scope of microbial diversity and their suite of metabolic functions remain challenging to link to ecosystem level processes due to methodological limitations.

For chapter 1 of my dissertation, I worked in collaboration with researchers at the University of Vienna using extensive literature searches to explore the different spatial scales at which we study microbial diversity and function with the goal of linking microorganisms and their role as drivers of higher level processes. This work suggests that the level at which microorganisms interact, termed the 'microbial consortium', is a key scale which provides insights into microbial diversity, function, and enables scaling up from the single cell to the ecosystem. In chapter 2, I applied complementary metagenomic techniques to the discovery of soil biological diversity, including bulk metagenomics and a pooled, cell-sorting approach coupled to high-throughput sequencing, termed mini-metagenomics. In combination, these approaches uncover the genetic diversity of elusive microorganisms at the Harvard Forest Long-Term Ecological Research (LTER) site. Together, these approaches have generated some of the highest quality metagenome assembled genomes (MAGs) to date from this LTER experimental site, and have revealed a swath of diversity beyond the organisms typically found in high abundance in the soil. I demonstrate how complementary metagenomic techniques facilitate the discovery of biological diversity by highlighting the expanded knowledge of potential intracellular bacteria in the phylum Bacteroidetes. In chapter 3, I characterize the metabolism of representatives in the phylum Acidobacteria subdivision 2, which are abundant in forest soils but have yet to be described as there are no available genome sequences in this taxonomic group. Finally, chapter 4 describes sixteen novel giant viruses which have been discovered in Harvard Forest soil for the first time in collaboration with researchers at the Joint Genome Institute. These expand knowledge of phylogenetic diversity of the nucelocytoplasmic large DNA viruses (NCLDV) by 21%, and further demonstrate the utility of complementary metagenomic approaches in uncovering diversity of elusive viral entities in addition to microbial life.

Observed changes at Prospect Hill, the longest-running soil warming experimental site at Harvard Forest, reveal increases in soil microbial respiration, increases in nitrogen mineralization, decreases in soil organic matter and decreases in the overall microbial biomass of these soils in response to warming. Based on these findings, we can expect similar changes to occur at the Barre Woods warming experiment, which was established at the Harvard Forest LTER site in 2002. Additionally, we may anticipate similar changes in temperate forest soils as the Earth's climate changes and surface temperatures continue to rise. With these changes, the microbial community must change and adapt to shifting nutrient and substrate availability, moisture conditions and changing soil structure. This dissertation work supports our understanding of the expansion of niches for soil microorganisms with oligotrophic growth strategies and flexible metabolism. These traits will enable soil organisms to cope with a nutrient-limited environment that is predicted to occur in response to long-term climate change.

DOI

https://doi.org/10.7275/hsq9-ph87

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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