New publication from Cassie Ettinger (aka @casettron) and others: Fungi in the Marine Environment: Open Questions and Unsolved Problems 

New paper from Cassie Ettinger in the Eisen Lab:

Full citation:
Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS. 2019. Fungi in the marine environment: open questions and unsolved problems. mBio 10:e01189-18.


Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

Definitely worth a look if you are interested in fungi and/or marine microbes.


New paper from the Eisen lab on MAGs from two thermal pools in Kamchatka (great work led by Laetitia Wilkins @M_helvetiae and Cassie Ettinger @casettron) 

A new paper just out from the lab:

Laetitia G. E. Wilkins & Cassandra L. Ettinger (co-1st authors), Guillaume Jospin & Jonathan A. Eisen. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Scientific Reports. volume 9, Article number: 3059

This was truly a remarkable piece of work led by Laetitia G. E. Wilkins & Cassandra L. Ettinger who are co-first authors on the paper.  Also contributing to the work was Guillaume Jospin, the lab bioinformatics guru. I will write a much longer “story behind the paper” about this in the next week or two but wanted to give a brief summary here.

This paper had its beginnings just after September 11, 2001.  Yes. that September 11.  We had a meeting planned in September in Yellowstone National Park that had to be delayed due to 9/11.  The meeting then happened in October.  The meeting was between a group of US researchers and a group of Russian researchers to plan an NSF proposal on comparing the microbes living in hot springs in Yellowstone with those living in hot springs in Kamchatka.  The meeting went well and eventually we got a grant from NSF’s Biocomplexity program for this work.

At the time I was at TIGR (The Institute for Genomic Research) and I had a minor role in the grant – I was supposed to do coordinate some metagenomic sequencing of samples from Kamchatka.  We got some samples from Juergen Wiegel from U. Georgia and did a small amount of Sanger sequencing of them but this was right around the time I moved to UC Davis and right around the time that TIGR kind of dissolved.  We did not end up writing a paper on that small amount of Sanger sequencing.  Years later, Russell Neches in my lab got interested in this project and went to Kamchatka with Frank Robb and others on a collecting trip. See some details about this trip and plans back then in this blog post.  Russell then coordinated some Illumina sequencing of the same DNA samples we had done Sanger sequencing for at TIGR.  And Russell did some preliminary analysis of the samples but did not end up writing up a paper on it.

Fast forward again to a few years ago and we decided in my lab to try and rescue orphan data and try to at least get the data into the public domain and, if it was of interest to someone, write a paper on the data.  We thus created some “Reboot” channels within the lab Slack site and Laetitia Wilkins and Cassie Ettinger decided to try and do something with the Kamchatka data.  And they did.  This is what led to this paper.

A few other notes I would like to make here.  This paper certainly is a testament to the remarkable work of Cassie Ettinger and Laetitia Wilkins as well as Guillaume Jospin who helped them with some of the informatics.  I am really proud to have them all in my lab.  In addition, this paper is a culmination of contributions of all sorts of people.  We tried to acknowledge many of them in the Acknowledgement section of the paper and I am posting that below for the record here.

We would like to thank Russell Neches (ORCID: 0000-0002-2055-8381) for the use of photographs taken on a trip to Kamchatka, Russia in 2012. We also would like to thank Elizabeth A. Burgess and Juergen Wiegel for providing JAE with the DNA used here. We are also grateful to Christopher Brown (ORCID: 0000-0002-7758-6447) and Laura Hug (ORCID: 0000-0001-5974-9428) for their help getting access to the genomes used in Figure 2. A special thank you goes to Alexandros Stamatakis (ORCID: 0000-0003-0353-0691), Wayne Pfeiffer and Mark Miller for offering their help with getting the CIPRES Science Gateway server to run RAxML-HPC2 v.8 on XSEDE. We also thank two anonymous reviewers for comments on earlier versions of this manuscript. A. Murat Eren (ORCID: 0000-0001-9013-4827) provided constructive feedback on the publicly available preprint version of this article. LGEW was supported by a fellowship of the Swiss National Science Foundation P2LAP3_164915. Funding for the sequencing at TIGR was provided by a a subcontract to JAE for a grant from the National Science Foundation (MCB-MO 0238407). Funding for some of the work on this project was also provided by grant from the Gordon and Betty Moore Foundation (GBMF5603) to JAE.

New preprint from lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka

A new preprint has been posted from the lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia | bioRxiv

Paper was led by Laetitia Wilkins and Cassie Ettinger (Guillaume Jospin and I are co authors).  


Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. Using a shotgun metagenomics approach, we assembled population-level genomes of bacteria and archaea from two pools using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and placed them in the context of the current microbial tree of life. We highlight MAGs representing previously underrepresented archaeal phyla (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study can be considered complementary to foregoing studies in the same ecosystem as it adds more comprehensive information about phylogenetic diversity and functional potential within this highly selective habitat.

I will try to write more about it later – I am so impressed by what Laetitia and Cassie did here.  This is what we call a “reboot” project in the lab – this was data that was generated and then not turned into a paper and was just sitting there.  A while ago we started a “reboot” program to start to try to turn such data sets into papers and they adopted this data set.  The data is Solexa shotgun metagenomic data from samples from hot springs in Kamchatka (yes, Solexa, read the paper for details).  The DNA used was leftover from an old project which included a collaboration with Juergen Wiegel’s lab (and some others) that had started, at least in terms of discussions, in 2001.  Anyway – I will try to write out more on the story behind this work soon.  But please, check out the paper, and feel free to provide feedback.