Presentation Title

The Effects of Site and Habitat on the Microbial Composition of California Soil Ecosystems

Start Date

November 2016

End Date

November 2016

Location

HUB 302-39

Type of Presentation

Poster

Abstract

Although we often focus on animals and plants when observing terrestrial ecosystems, soil organisms play a key role in defining the characteristics and diversity of an ecosystem. In the past, soil organisms were not well-studied because many microorganisms could not, and still cannot, be cultured. Recently, however, DNA sequencing has been under investigation as a new method of studying microorganisms in the soil. In our experiment, we collected soil samples and performed DNA sequencing in order to observe trends in bacterial species composition.

Soil samples were collected from the California sage scrub and grassland ecosystems of the Santa Monica Mountains (SMM), Bernard Field Station (BFS), and Crafton Hills (CH). In order to observe the effects of the non-native grassland invasions on bacterial compositions, we first performed amplicon sequencing on DNA extracted from the soil samples. Then, we analyzed the sequences with differential abundance analyses, principal component analyses (PCoA), alpha diversity estimates, and PERMANOVA using Rstudio.

In general, site (SMM, BFS, CH) seems to have a greater influence on microbial diversity than habitat (grassland v. sage scrub). From the PCoA, we see that the samples are well-separated by site and generally separated by habitat except at the BFS. Similarly, BFS had the least statistically significant differences between its habitat samples in the differential abundance plots. This could be due to the fewer number of OTUs observed in the BFS samples, possibly from its sandy soil composition. Furthermore, according to the PERMANOVA, site has a slightly larger influence on diversity compared to habitat, as supported in the PCoA and Alpha Diversity Measures. In the future, we plan to perform analyses measuring the presence or absence of species in each sample and find ways to characterize the role of these present or absent organisms using methods such as observing functional genes.

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Nov 12th, 1:00 PM Nov 12th, 2:00 PM

The Effects of Site and Habitat on the Microbial Composition of California Soil Ecosystems

HUB 302-39

Although we often focus on animals and plants when observing terrestrial ecosystems, soil organisms play a key role in defining the characteristics and diversity of an ecosystem. In the past, soil organisms were not well-studied because many microorganisms could not, and still cannot, be cultured. Recently, however, DNA sequencing has been under investigation as a new method of studying microorganisms in the soil. In our experiment, we collected soil samples and performed DNA sequencing in order to observe trends in bacterial species composition.

Soil samples were collected from the California sage scrub and grassland ecosystems of the Santa Monica Mountains (SMM), Bernard Field Station (BFS), and Crafton Hills (CH). In order to observe the effects of the non-native grassland invasions on bacterial compositions, we first performed amplicon sequencing on DNA extracted from the soil samples. Then, we analyzed the sequences with differential abundance analyses, principal component analyses (PCoA), alpha diversity estimates, and PERMANOVA using Rstudio.

In general, site (SMM, BFS, CH) seems to have a greater influence on microbial diversity than habitat (grassland v. sage scrub). From the PCoA, we see that the samples are well-separated by site and generally separated by habitat except at the BFS. Similarly, BFS had the least statistically significant differences between its habitat samples in the differential abundance plots. This could be due to the fewer number of OTUs observed in the BFS samples, possibly from its sandy soil composition. Furthermore, according to the PERMANOVA, site has a slightly larger influence on diversity compared to habitat, as supported in the PCoA and Alpha Diversity Measures. In the future, we plan to perform analyses measuring the presence or absence of species in each sample and find ways to characterize the role of these present or absent organisms using methods such as observing functional genes.