Category Archives: Marine Fungi

Preprint available: Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids


Seagrasses are globally distributed marine flowering plants that are foundation species in coastal ecosystems. Seagrass beds play essential roles as habitats and hatcheries, in nutrient cycling and in protecting the coastline from erosion. Although many studies have focused on seagrass ecology, only a limited number have investigated their associated fungi. In terrestrial systems, fungi can have beneficial and detrimental effects on plant fitness. However, not much is known about marine fungi and even less is known about seagrass associated fungi. Here we used culture-independent sequencing of the ribosomal internal transcribed spacer (ITS) region to characterize the taxonomic diversity of fungi associated with the seagrass, Zostera marina. We sampled from two Z. marina beds in Bodega Bay over three time points to investigate fungal diversity within and between plants. Our results indicate that there are many fungal taxa for which a taxonomic assignment cannot be made living on and inside Z. marina leaves, roots and rhizomes and that these plant tissues harbor distinct fungal communities. The most prevalent ITS amplicon sequence variant (ASV) associated with Z. marina leaves was classified as fungal, but could not initially be assigned to a fungal phylum. We then used PCR with a primer targeting unique regions of the ITS2 region of this ASV and an existing primer for the fungal 28S rRNA gene to amplify part of the 28S rRNA gene region and link it to this ASV. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. This clade includes known parasites of freshwater diatoms and algae and it is possible this chytrid is directly infecting Z. marina leaf tissues. This work highlights a need for further studies focusing on marine fungi and the potential importance of these understudied communities to the larger seagrass ecosystem.

Marine Fungi Workshop

I just returned from a marine fungi workshop set up by Amy Gladfelter and supported by the Gordon and Betty Moore Foundation. The workshop was from May 7-9th at the Marine Biological Laboratory in Woods Hole, MA. This was actually my second trip to Woods Hole, my first was in summer of 2015 to attend the Microbial Diversity course (click here to read a cheesey poem I wrote about the course).

The workshop started with everyone giving 5 minute lightning talks about their research. It was my first time presenting my research ideas to people outside of UC Davis and even though it was only a 5 minute presentation, I was scared to death. I am pretty sure I was literally shaking in the moments leading up to my talk and my imposter syndrome was yelling at me to run far far away so that the real mycologists (doubly scary since they were mostly all professors) wouldn’t know they’d invited a eco-evolutionary microbiologist / bioinformagician into their midst. I can’t really remember anything that happened in those 5 minutes, but I walked away feeling like I had crushed it (take that imposter syndrome).

After the talks, we discussed what we thought were some big issues in marine mycology as a group before breaking up into 4 smaller groups with the goal of drafting white papers on these issues.

The 4 smaller group topics were:

  1. Who is out there? Identification and isolation of fungi from different parts of the marine environment
  2. How can marine fungi be studied? Establishing model systems to discover new biology
  3. What are fungi doing to influence the geochemical cycle of the ocean? Establishing the function of fungi in chemical cycling and contributions to climate
  4. How are fungi interacting with and shaping the marine biosphere? Identification of fungal interactions across scales of life in the ocean
Some of the dominant themes that resulted from these conversations were (1) a desire to  inform both scientists and non-scientists of the presence of fungi in the ocean; (2) to impart and quantify the importance of the roles of marine fungi in the ocean; (3) the unclear definition of marine fungi and whether or not this definition includes facultative marine fungi, transient terrestrial fungi or freshwater / brackish fungi; (4) our current lack of understanding of the genetic, phylogenetic, functional and ecological diversity of marine fungi and the spatial scales at which they exist in the marine environment; (5) the lack of standardized protocols for the study of fungi more generally and a need for improved / expanded databases for fungal sequence data that potentially incorporate phylogeny.

I got to meet a bunch of awesome people from a variety of fields (including systematics, cell biology, genetics, chemistry, bioinformatics, etc), some of whom I had heard a lot about / seen before on twitter and others who were completely new to me! I only wish it had been 1-2 days longer to further promote networking opportunities and collaborative discussions. Despite the jam-packed workshop schedule, we somehow managed to fit in a boat trip on one of the MBL’s collection vessels, the Gemma.

Throughout the conference, I realized a few things (1) I should probably be going to and giving talks at more conferences; (2) networking skills are extremely important; (3) I need to learn more about fungal taxonomy and systematics; (4) I am now super excited to look at and incorporate fungi in some of my other non-seagrass projects; (5) working on my computer on a bus is not a good idea and makes me extremely motion sick.
Found some microbes in Woods Hole, but no marine fungi 😦
This workshop served as a breathe of fresh air for me and helped renew my excitement for analyzing my seagrass-associated fungal ITS data. It also gave me a few cool ideas of things to do moving forward. I am extremely grateful that I had the opportunity to attend and that the Moore foundation was able to bring us all together. I can’t wait for the next marine fungi meet-up!