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Microbial community diversity, function, and succession in California’s Mediterranean habitats


We live on a predominantly microbial planet. I it is estimated that more than a billion microorganisms can live in a gram of soil. Microorganisms comprise the largest pool of genetic diversity on the planet and drive global biogeochemical cycles. Since microbial ecology is intimately associated with environment, changes in environmental conditions can have profound effects on the microbial diversity and function of microbial communities. In this dissertation I study; 1) the relationship between environmental heterogeneity and microbial diversity, 2) the relationship between the environment, microbial diversity, and microbial functional traits, and 3) microbial secession related to changing environmental conditions during anaerobic decomposition.

Chapter 1

Annual grassland invasions can increase environmental heterogeneity and reduce the biological diversity of plants and animals. There is a generally positive relationship between environmental heterogeneity and biodiversity, and more specifically, soil heterogeneity is known to influence plant diversity. Here I test if the diversity of soil microorganisms, like that of plants, displays a positive relationship with soil environmental heterogeneity. Specifically, I test to see if invasive annual grasses lead to reductions in soil heterogeneity and microbial alpha- and beta- diversity. I sampled the soil profile across invasive annual grassland, oak woodland, and coastal sage scrub habitat and characterized environmental heterogeneity (soil percent carbon, nitrogen, water content, total dissolved solids, and pH in addition to litter percent carbon, nitrogen and C:N), alpha and beta diversity. I found that invasive annual grassland habitat has greater soil environmental homogeneity than native woody habitats throughout the soil profile. Annual grassland communities have lower alpha-, but not beta-, diversity than native woody species. Patterns of alpha diversity with depth differ between grassland and woody habitat, and although not significant, woody habitats have higher community heterogeneity. Alpha diversity and beta diversity show positive relationships with several measures of environmental heterogeneity, suggesting that like plants, soil microbial diversity increases with environmental heterogeneity. Annual grassland invasions into native woody habitats reduce soil microbial diversity. This is particularly true in deep soil communities.

Chapter 2

Plant invasions frequently alter ecosystem processes in part because they modify soil microbial communities. These communities decompose the bulk of terrestrial organic matter by producing and releasing extracellular enzymes. California's native Mediterranean habitats (e.g. Oak woodland and coastal sage scrub) are invaded by annual grasses and are converted to invasive annual grasslands. I investigated the relationship between extracellular enzyme activities and microbial community composition in these habitats by examining 1) how extracellular enzyme activities differed between native and invasive habitats, 2) whether changes in microbial community correlate with changes in extracellular activity, and 3) if the composition of bacterial phyla that contain genes for extracellular enzymes differ between habitats. I found that annual grassland enzyme activities are much different from those of woody habitat, and the differences in enzyme activities between habitats generally declined with depth as did enzyme activities. There was also a strong correlation between community composition and extracellular enzyme activity. This correlation was not influenced by soil environmental variables. The relative abundance of phyla with genes for extracellular enzymes were similar between habitats and those genes are contained in distinct assemblages of phyla. Habitat change through annual grassland invasion modifies soil communities and their functions thought out the soil profile. Future studies on the effects of annual grassland invasion on ecosystem processes in deep soil are needed to fully understand the consequences of these invasions.

Chapter 3.

Natural tar seeps are the source of millions of fossils from animals that became entrapped, died and were decomposed over the millennia. The microbial communities responsible for the anaerobic decomposition of these entrapped animals are not known. However, microbial communities likely play a role in the rapid time to skeletonization of animal components submerged in tar. I hypothesized that high energy animal tissue would support fast growing taxa and support lower microbial diversity, and that microbial succession across different locations in the tar environment and animal tissue decay would resemble known patterns of microbial decomposition in similar habits. I sampled different locations in a tar seep and also bobcat limbs that were experimentally submerged in the seep and left to decay until skeletonization. Microbial communities were characterized using 16S rDNA sequencing of the V4 region. I found that decay communities had lower diversity than tar environment communities and that microbial succession proceeded similarly to that in analogous habitats. The addition of animal tissue into this tar seep appeared to lead to rapid microbial community succession. This microbial succession likely affected the rate of decomposition of this tissue. Future experiments are required to understand the role of microbial succession in determining the rate of decomposition and time to skeletonization in tar environments.

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