Haloferax volcanii, model archaea, and me

When I was a graduate student I was looking around for an extremophile – especially an evolutionarily novel one.  And I settled on this species Haloferax volcanii – a model halophilic archaeon largely because Ford Doolittle and colleagues had started to turn it into a genetic model organism (and because Patrick Keeling, from Ford’s lab convinced me it was a good thing to do).  So I started work on this species – doing DNA repair studies in the lab.  See my PhD thesis for some of the work I did which I never published outside of the thesis for multiple reasons.  But I continued to be interested in this species.  And when I was working at TIGR, an NSF Program Officer approached me asking me to help get the genome sequencing done for this species.  So, well, I did: The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.  And I became interested in other haloarchaea and eventually started working with Marc Facciotti, in the lab next to mine, in sequencing from across the diversity of the haloarchaea: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response.

Anyway – enough about me.  The whole point here is to point people to a new paper:  BMC Biology | Abstract | Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery.  Further evidence for the use of Haloferax volcanii as a model species.  Tools continue to become available for genetic and experimental studies in this species.  So – if you are looking for an unusual and interesting organisms to work on – consider working on this species …

Story behind the paper: Bonnie Baxter on "A tale of salt and gender" #STEMWomen #Halophiles

After posting A tale of salt and gender: participation of women in halophile research I sent the post to Bonnie Baxter, one of the authors of the article I discussed and I asked if she would be interested in writing a guest post about the “Story Behind the Paper” (for which I have a whole series).  I am so so pleased that she said yes.  I have followed Bonnie’s work for many years but this is her first guest post here.  I hope there will be more.  She is a wonderful and brilliant scientist and educator.

Guest Post by Bonnie Baxter
Salty Sisters: The Women of Halophiles

Bonnie Baxter and Nina Gunde-Cimerman at the north arm of Great Salt Lake (2008)
I was drawn to the western US, the extreme landscapes, and ended up at the only liberal arts college in Utah. I had wanted a career doing science with undergraduates, and I set about exploring the microbiota of Great Salt Lake. Since few had studied this incredible spot, I quickly became the go-to person for studies on the lake, and these collaborations and grant projects eventually evolved into an organization I direct called Great Salt Lake Institute. We are dedicated to research, scholarship and education efforts on Great Salt Lake.
There had been no microbiology done on Great Salt Lake since 1979. This is why there was much excitement concerning our emerging data, and in 2004, I was invited to speak at the triennial International Halophiles conference in Slovenia. Halophiles are microbes that thrive at high-salt, and the people who study them maintain an interesting balance of field-work and lab work. I had been to large meeting on DNA repair, DNA replication, nucleases and the like, but I had never met a group who were centered on a theme that connected them around the planet. 
From my first Halophiles meeting (I’ve since attended 2007 in Colchester UK, 2010 in Beijing and 2013 at University of Connecticut), I felt an unusual level of support from the elders of this group. And I noticed that, unlike the NASA meetings or biochemistry meetings I attended, there seemed to be a nice balance of men and women. There were a group of folks who had participated for a long time, without a membership organization, and these people maintained the notion of mentoring in the field. It is this spirit that drew all of us younger folk to participate. 
At each of the International Halophiles conferences, there is typically a history talk that brings forth work from past scientists from the field. After an evening in Beijing, I lamented to Aharon Oren, who studies microorganisms of the Dead Sea, that I found his history talk very engaging, but he seemed to overlook the contributions of women. So he challenged me to give the next history talk in Connecticut. By the next morning, at our shared 6 am breakfast, Aaron gave me a list of 20 or so women he thought has contributed great things to the halophile field. I had been given a challenge, and I accepted. I invited an accomplice to the project, Nina Gunde-Cimerman, from University of Ljubljana, Slovenia, and we began our research.
Bonnie Baxter says “My daughter thought it was more appropriate if we dressed this way for the talk.  But this is not the way female scientists do their work…”
Given my connection to Great Salt Lake, I’ve been asked to give an unusual number of keynote addresses and special talks (for a professor at a liberal arts college). I have often been the only female speaker at a meeting, or the only woman on a national committee. Since graduate school, I have held an interest in exploring why there are underrepresented groups in science. Why is retention in STEM fields different for men and women? Why are women underrepresented as physics or mathematics professors in the US, but hardly at all in Russia or Italy? This is what drove me to undergraduate science, fixing these problems and better understanding them. 
In the summer of 2013, Nina and I gave the opening talk at the International Halophiles conference at UConn, entitled “Salty Sisters: The Women of Halophiles.” The talk included our analysis of the participation of women in these conferences since 1978. 
After reading many studies of women underrepresented as speakers, we were shocked that our numbers were very different. It appeared that the halophile organizers had done an excellent job of gender inclusion, relatively speaking. Following the talk, and for weeks afterward, many scientists (male and female) approached us, telling us their experiences as women in the field or discussing how important this topic was.
Nina Nina Gunde-Cimerman and Bonnie Baxter
We were thus inspired to publish a manuscript from the lessons we learned. As we looked at recent comparative studies, we learned more, in particular, the gender bias involved in speaker or author invitation. Please see the manuscript introduction for this important overview. Several publications pointed at the underrepresentation of women in invited speakers or authors for invited reviews. In problem-solving mode, Casadevall and Handelsman (2014) demonstrated that the inclusion of women on the organizing committee is critical to a balanced speaker docket.  
Bonnie, Aharon and Nina, Beijing 2010
What we learned as we analyzed the conference participation in our field, is that we were doing quite well in gender balance of invited speakers, 36% of the speakers were women since 1978! And indeed, women had been included in many of the organizing committees. We saw a 10-16% increase in female speakers when this was the case. We also came to understand that there was a small group of scientists who were committed to holding this conference with no organizational funding. This led to cooperation, collaboration, avid mentorship and strong friendships. This was a group that welcomed women, young scientists and peoples of all nations. I daresay that this is not always the situation in a particular field as the “village elders” may work by competition, not cooperation. These halophile elders, for example, worked to get external funding at each meeting to bring graduate students and post-docs to the conferences with little cost. 
Recent studies on gender bias in science are focused on numbers we can measure and methods to resolve the problem. Jon Eisen has been a strong proponent for what is becoming a national movement to require organizing committees to have written policies that include gender equity.  Scientists, male and female, should request this document and refuse to participate if it is not produced. 
The co-authors and I were so pleased to report a positive example in a sea of negative ones. I hope that this groupsof salty scientists can inspire others to build communities of inclusion as we learn from each other in exploring the natural world.

A tale of salt and gender: participation of women in halophile research

Interesting paper on women in science of direct relevance to my work: Frontiers | Salty sisters: The women of halophiles | Extreme Microbiology.  I have been working on halophilic archaea for many years (since introduced to them in graduate school) and published papers on this topic (e.g., see The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon and Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux and more coming).  However, I have never been to a meeting dedicated to the topic and confess I have not thought specifically about the gender of scientists in this field and at meetings in the field and such.  Thus I was pleasantly surprised to see this analysis from Bonnie Baxter, Nina Gunde-Cimerman and Ahoren Oren.  Their abstract is below:

A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.

As part of their paper they analyze participation of women at conference on halophiles:

This is a useful analysis and compendium and it would be great to see this done for as many fields as possible. 

Story behind the paper guest post by Corey Nislow (w/ Metka Lenassi) on "Genomics w/o Borders"

Below is another in the “Story behind the paper” series of guest posts here.  This one is from Corey Nislow w/ Metka Lenassi.  If anyone else has published an open access paper on anything relating to this blog and would like to write a guest post on the Story behind the paper, please let me know.

Genomics without Borders: Genome Sequence of the Extremely Halotolerant Yeast Hortaea werneckii 

by Corey Nislow (with Metka Lenassi)

In this guest post (thank you Jonathan!) I wanted to tell the story behind a paper that my colleagues and I published two weeks ago in PLoS ONE. The story also offers an opportunity to talk about what role, if any, a middle author can play in a scientific study.

The story is set in Slovenia a beautiful country which was part of the former Yugoslavia and which is home to about 2 million inhabitants, 2400+ fungal species (thanks Wikipedia) and some very interesting environments. One of these environments is the Secovlje Salterns where one can find the yeast Hortaea werneckii.

A worker harvests sea salt in the Secovlje salterns, July 17, 2010. Some 2600 tons of salt is expected to be produced during the two and a half month season at the salterns.(Xinhua/Reuters Photo)

I hadn’t heard of Hortaea until I started googling around looking for a yeast extremophile that I can grow in the lab to dissect out its nucleosomes to ask questions regarding nucleosome occupancy and transcription in the face of extreme environments. Turns out it was not a crazy idea–

13 years ago a peculiar black yeast Hortaea werneckii was isolated from its natural habitat: waters containing so much salt, it would kill most living organisms instantly. Since then, two small (but enthusiastic) Slovenian groups have tried to understand its halotolerance. This demanded field trips to the beautiful Slovenian coast, but also a lot of hard work and inventiveness to optimizing protocols used for other organisms – and to do it on a low budget. The first important obstacle was actually cultural – to persuade the scientific community that such extreme yeast even exists in nature! You can see it below. We now have ample evidence as Hortaea has been isolated from many seawater-related environments, saline lakes, but also from surface layers of tropical microbial mats in salterns and even from spider webs in Atacama Desert caves. All these different Hortaea strains are now waiting in their freezer (the Ex culture collection) to be analyzed.

Hortaea werneckii growing happily on 2M salt.

The figure below summarizes what was known about halotolerance of Hortaea before the genome sequence was decoded. In brief, high salinity is detected by sensors of the HOG signaling pathway (green arrows), which modulate the expression of salt-responsive genes (underlined green). The expression of other genes also varies; genes with higher expression at high salinity are written in red, repressed genes in blue). The impact of a hyperosmolar environment is countered by increasing the energy supply to drive energy-demanding processes such as export of Na+ and H+, import of glycerol andthe synthesis of compatible solutes. Melanization of the cell wall reduces the leaking of solutes from the cells and restructuring of membrane lipids helps preserve the integrity of the cells. Read this paper if you want to know more: Gostinčar et al, Adv Appl Microbiol. 2011;77:71-96 .

Gostinčar et al, Adv Appl Microbiol. 2011;77:71-96

This critter, as our recent paper reports, is as interesting genotypically as it is phenotypically. The full genome sequence reported in the PLoS ONE paper shows that genome size is 51mB quite a bit larger than its closest relatives, and given the number of gene models detected (20,000!), for all intents and purposes it looks like Hortaea underwent whole genome duplication last weekend!

Piquing my interest, I immediately started searching for the the genome sequence to have a reference to map nucleosome sequencing reads. Turns out, I had requested the strain from Metka years ago, only to find that one of our lab mates, Uros, with whom I was collaborating at the University of Toronto, had performed some of the groundwork on Hortaea for his PhD. But the network connections don’t stop here, I moved to the University of British Columbia last year, and as it happened Hortaea is popular in Vancouver too! Our new colleagues at UBC were working together with the Slovenian team on sequencing and analyzing the Hortaea genome. In fact, the collaboration started in 2005, catalyzed by a poster at the Budapest FEBS conference were Metka, at that time still a PhD student, and Ivan Sadowski started a discussion about the interesting phenotypic switch that Hortaea undergoes between yeast and filamentous forms. So, by virtue of a convergence of curiosity, good luck and generous collaborators I had the good fortune of being an active participant in the study.

So how does this have anything to do with what a middle author does or doesn’t do on a manuscript? And why do I care? 

Well, I recently re-read the comments section of a fellowship application, and ginned up the guts to read the “supervisor/training environment” section. The chief criticism was that I have a lot of papers on which I am not the senior author. So to the skeptics, I would say- even middle authors play important roles in bringing a study to an audience. In my case my self-interests guided my actions, but along the way, I had the chance to learn about an extraordinary critter, and an amazing group of Slovenian scientists. Yeah, I needed the genome sequence, but I was also excited to help drafting the manuscript, have our sequencing facility prepare additional libraries to close some gaps, and now to bring attention to this extraordinary critter.

The genome sequence offers an exciting new start in studies of Hortaea werneckii. Going forward, the Slovenians want to study its transcriptome and proteome in response to increasing salinity. Preparing knock-out mutants is also a must, to find key genes important for halotolerance. We definitely want to take a closer look at all those cation transporters and their functions. It would also be fun to find its mating partner in one of those frozen Hortaea samples. And now that the genome sequence is available to everybody, the research on this extremely interesting species may start to gain more appeal even to researchers beyond the two stubborn Slovenian groups.

Although I might not get to Slovenia in the foreseeable future, I wouldn’t be surprised if one of my graduate students will meet up with the group at an upcoming yeast meeting. This particular student is dragging our lab into evolutionary genomics by trying to see if he can’t get Hortaea to lose some of its genome in long-term culture (I can’t help but think of “Amadeus” where Salieri is telling Mozart that the composition is fine but it has too many notes….). I’m sure the results will be surprising, and am also encouraged to see what our future collaboration will bring.

Halophiles 2013 Conference

Forwarding this:

Dear colleague,

You are cordially invited to participate and submit an abstract to the 10th international congress on halophilic microorganisms – Halophiles 2013, which will be held on the campus of the University of Connecticut, Storrs from June 23rd – 27th 2013.

This conference will bring together an exciting cohort of scientists from many fields of halophile research including but not limited to biodiversity, evolution, ecology, astrobiology, biogeochemistry, biochemistry, physiology, protein structure/function, genetics, genomics, metagenomics, and biotechnology.

Please visit our website for more details. www.regonline.com/halophiles2013

Key Dates:
Deadline for Abstract Submission – April 30th
Deadline for canceling with full refund – May 24th
Deadline for canceling 50% refund – June 7th

Please, kindly forward this invitation to your colleagues.

Thane Papke, Organizing Chairpeson

Halophiles 2013 Conference June 23-27 U Conn.

Just got this from Thane Papke

It is my pleasure to invite everyone to the tri-annual Halophiles conference on microorganisms. This year’s event will take place from June 23-27th on the Storrs Campus of the University of Connecticut.

The conference will highlight the diverse research of over 30 invited speakers on topics of biodiversity, evolution, proteins, biochemistry, physiology, genetics, applied biotechnology, astrobiology, ecology and biogeochemistry, and there will be a joint meeting of the ICSP-Subcommittees on the taxonomy of the Halobacteriaceae and Halomonadaceae.

If you are interested in participating, please go to the following website for registration, and more information. http://www.regonline.com/halophiles2013

This announcement was made from an incomplete email list and cannot reach everyone. If you are aware of any names who should receive this and future announcements, please forward this notice to them, and let me know their address and I will add them to the list. If you are on the list and wish to be removed, please let me know.




PLoS One Beta is released – a new way to publish and discuss scientific papers

Well just got an email from Chris Surridge of PLoS One saying their Beta Site is open to the public. I am excited by this new journal and system and plan to submit many of our papers there. People should check it out for themselves and hopefully give comments to them to make the system better. Some detail from the email is given below.

The first paper there that struck my eye is a paper on polyploidy in halophilic Archaea. This paper, by Sebastian Breuert, Thorsten Allers, Gabi Spohn, and Jörg Soppa suggests that polyploidy is more common in archaea than was previously appreciated.

The email says:

Before your first visit, I want to let you know about the inherent challenges of this project and the philosophy that compels PLoS to confront them.

We want to speed up scientific progress and believe that scientific debate is as important as the investigation itself. PLoS ONE is a forum where research can be both shared and commented upon – we are launching it as a beta website so that the whole scientific community can help us develop the features.

What makes the site beta? Not the content, which features peer-reviewed research from hundreds of authors across a diverse range of scientific disciplines. It’s the additional tools and functionality surrounding these papers that will be continually refined and developed in response to user feedback.

It is this union of continually evolving user tools provided by the Topaz publishing platform and extensive content that will make PLoS ONE a success.


The first beta release of PLoS ONE features tools that allow users to annotate articles and participate in discussion threads. Our goal is to spark lively discussion online and we’d like to invite you to participate. Future updates will include user ratings for both papers and the comments made about them, personalized content alerts and much more.

We will be watching with interest to see how our new platform and software responds to high volumes of traffic and encourage you to give your feedback on your first experience via the site itself.