Taxonomic Diversity of the Bacterial and Fungal Communities Associated with the Seagrass, Zostera marina

Abstract

Seagrasses are the fully submerged marine angiosperms (flowering plants) and are foundation species that play important ecological roles in primary production, food web support, and elemental cycling in coastal ecosystems. Sometimes referred to as the “whales of the plant world”, there are three main lineages of seagrass that adapted independently to the marine ecosystem through convergent evolution. Although plant-microbe interactions are important for land plant fitness, little is known about how microbial communities associated with marine plants may affect plant health and what abiotic and biotic factors affect the composition and function of these communities.

For the first part of my dissertation, I investigated abiotic factors affecting the composition of the bacterial community associated with the seagrass, Zostera marina. This involved three studies, (1) an investigation of the bacterial community associated with plants at different locations within a seagrass patch, (2) an investigation of whether proximity to a marina is correlated with the taxonomic composition and structure of the seagrass microbiome, and (3) a survey of the bacterial community in seagrass-associated sediment during ammonification, the first step in early remineralization of organic matter. In the first study, I found that bacterial community composition differed significantly between seagrass roots, leaves and sediment. I also found that sediment bacterial community composition differed between locations within a patch and that these differences correlated with seagrass density. In the second study, I found no significant differences in microbial community structure or composition at different distances from the Bodega Bay marina. In the third study, I saw that the microbiome of sediment from different experimental field plots followed similar successional patterns during the process of ammonification, which seemed to be due to changes related to sulfur cycling and metabolism. However, I was not able to identify any correlation between bacterial community composition and the rate of ammonification or Z. marina genetic diversity in field plots.

For the second part of my dissertation, I focused on the fungal community associated with Z. marina. Fungi are often neglected in microbiome studies and marine fungi are generally understudied. This involved three studies, (1) a characterization of the fungal community at a local scale (Bodega Bay, CA) using high throughput sequencing of the internal transcribed spacer (ITS) region, (2) culturing and identification of fungal isolates associated with Z. marina, and (3) an investigation of Z. marina mycobiome at a global scale using high throughput sequencing of the 18S rRNA gene and ITS regions. In the first study, I found evidence of relatives of terrestrial fungal endophytes (Colletotrichum sp.) associated with Z. marina. I also found that there were many fungi associated with Z. marina locally for which there were only distant taxonomic matches in existing databases, and that many of these distant matches were to understudied lineages of fungi, including the Chytridiomycota and Aphelidomycota. In the second study, I generated a fungal culture collection of 108 isolates associated with Z. marina, including representatives of Colletotrichum sp. In the third study, at a global scale, the fungal community appears to be locally adapted, in that many of the fungal taxa found in association with Z. marina are only found at one location. Additionally, we again observed that many fungal taxa observed were members of understudied fungal lineages (e.g. Chytridiomycota).

My dissertation has helped lay a foundation for future seagrass-microbiome studies and highlights the need for further studies focused on the potential functional importance of understudied communities, like marine fungi, to the larger seagrass ecosystem.