Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Biochemistry

First Advisor's Name

Dr. DeEtta Mills

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Dr. Bruce McCord

Second Advisor's Committee Title

Committee Member

Third Advisor's Name

Dr. Laurie Richardson

Third Advisor's Committee Title

Committee Member

Fourth Advisor's Name

Dr. Mauricio Rodriguez-Lanetty

Fourth Advisor's Committee Title

Committee Member

Fifth Advisor's Name

Dr. Yuk-Ching Tse-Dinh

Fifth Advisor's Committee Title

Committee Member

Keywords

carbon cycle, functional genes, microbial diversity, GeoChip functional microarrays, soils, Miami-Dade County, correlation network analysis

Date of Defense

11-2-2016

Abstract

Decomposition of soil organic matter by microbial processes results in carbon sequestration within soils and/or carbon loss via atmospheric emission of carbon dioxide and methane. Natural as well as anthropogenic factors have been documented to impact soil microbial diversity and the associated biogeochemical functions. The soil microbial communities co-inhabiting Miami-Dade County soils, Florida are under threat because of the ongoing restoration efforts in the adjoining Florida Everglades Parks, predicted climatic changes such as sea-level rise and high rainfall, as well as urbanization. Therefore, an improved understanding of the current microbial functional communities is essential to better assess the impact of soil communities when anthropogenic or climatic disturbances occur. The objectives of the current study were to characterize the biodiversity and distribution of: a) cellulose degrading microbial community, and b) methanogenic guilds responsible for producing the gas methane, across four different Miami-Dade County, Florida soil types using the high throughput technique of GeoChip 5.0 functional microarray. In addition, the influence of vegetation cover, organic content, soil moisture content, pH, and soil texture in shaping the soil functional microbial community was also investigated. The function of cellulose degradation was distributed across wide range of taxonomic lineages with the majority belonging to the bacterial groups of Actinobacteria, Firmicutes, Alphaproteobacteria, and Gammaproteobacteria, whereas Ascomycota and Basidiomycota were the only detected fungal phyla. The cellulolytic bacterial community correlated more with the vegetation cover while fungal groups showed influence of moisture and organic content as well as percent silt. Six out of the seven methanogenic orders, with the greatest numbers found in the Methanomicrobiales, Methanosarcinales, and Methanomassiliicoccales, were identified across all four soil types of Miami-Dade. The abundance of the mcrA gene sequences was significantly greater with respect to soil moisture content. Additionally, the recently classified order Methanomassiliicoccales was identified across all four soils, including soils with lower moisture content not thought to provide ideal redox conditions to support methanogens. The greater number of correlation network interactions amongst the methanogenic guilds in the Florida Everglades wetlands versus the urbanized Miami-Dade County soils depicted the impact of the historical drainage of the Florida Everglades on the methanogenic community. Overall, the current study characterized the biodiversity of cellulolytic and methanogenic organisms across dry and saturated soils of Miami-Dade County and demonstrated that microbial guilds were functionally redundant and were influenced to some extent by the soil abiotic factors. Also, results from network analyses provide a platform to assess the future impacts of disturbances on the microbial community.

Identifier

FIDC001222

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