Tag: marine microbiology

Moore Foundation: Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

Got this from the Gordon and Betty Moore Foundation and they said I could post it here.

Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

Marine Microbiology Initiative Gordon and Betty Moore Foundation November 21, 2014

The Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation aims to enable scientists to uncover the principles that govern the interactions among microbes and that influence nutrient flow in the marine environment. MMI is targeting closing gaps in and supporting the advancement of experimental model systems in microbial oceanography to enable new ways to uncover fundamental biological mechanisms.

We are soliciting expressions of interest (EOIs) for early-stage research projects to develop methods to genetically manipulate marine microeukaryotes as a first step in breaking current bottlenecks in the advancement of experimental model systems. MMI has two primary foci for this expression of interest:

  1. Development of genetic tools for diatoms. Diatoms are key players in the world’s oceans, generating ~20% of the world’s organic carbon, and a strong community of researchers is in place suggesting broad use of successfully developed methods. We are specifically interested in projects to develop reverse and/or forward genetics.
  2. Screening laboratory-scale culture collections for transformable marine microeukaryotes.

MMI will also consider projects to develop genetic tools and methods with other microeukaryotes that show promise for expanding the way the field can test hypotheses. If your idea does not fit category 1 or 2 above, please contact us prior to submitting your EOI.

MMI encourages EOIs from “inter-organismal” teams of researchers – i.e., complementary groups that have experience in a well-established model system and with a microeukaryote that is not currently genetically tractable – whose collaborative effort will bring innovative approaches to the field.

MMI invites you to send an expression of interest via email that briefly outlines a research project (one paragraph or less), using the following template:

  1. The lead researcher’s name, institution, and expertise.
  2. Indication of focus on genetic tools for diatoms (category 1 above) or laboratory culture screening for transformability (category 2 above).
  3. For category 1, the name of the organism(s); or, for category 2, the taxonomic group(s) to be screened. 
  4. A methodological or technical challenge that is hindering the development of a genetically manipulable marine microeukaryotic system that is ripe for solving and how you would address this challenge (3-5 sentences).
  5. The research team that would tackle this challenge, and why each team member’s expertise is relevant (one sentence per team member; please include institutional affiliations).

The opportunities that best align with MMI’s strategies and goals will be invited to submit proposals. MMI has allocated $7–10M to support this effort and anticipates making multiple, 2–3 year awards beginning in mid- 2015.

 Please submit your EOI by Tuesday January 6, 2015 to Samantha Forde at samantha.forde@moore.org.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

People not Projects: the Moore Foundation continues to revolutionize marine microbiology w/ its Investigator program

People not Projects.

It is such a simple concept.  But it is so powerful.  I first became aware of this idea as it relates to funding scientific research in regard to the Howard Hughes Medical Institute’s Investigator program.  Their approach (along with a decent chunk of money) has helped revolutionize biomedical science.  And thus I was personally thrilled to see the introduction of this concept in the area of Marine Microbiology a few years back with the Gordon and Betty Moore Foundation’s “Marine Microbiology Initiative Investigator” program.  Launched in 2004 it helped revolutionize marine microbiology studies in the same way HHMI’s investigator program revolutionized biomedical studies.

The first GBMF MMI Investigator program ran from 2004 -2012. And the people supported were pretty darn special:

Now I am I suppose a little biased in this because at the same time GBMF launched this program they also put a bunch of money into the general area of Marine Microbiology and I have been the recipient of some of that money.  For example, I got a small amount of money as part of the GBMF Funded work at the J. Craig Venter Institute on the Sargasso Sea and Global Ocean Sampling metagenomic sequencing projects and also had a subcontract from UCSD/JCVI to do some work as part of the “CAMERA” metagenomic database project.  I ended up being a coauthor on a diverse collection of papers associated with these projects including Sargasso metagenome and this review, and GOS1, GOS2 and my stalking the 4th domain paper.

I am also a bit biased in that I have worked with many of the people on the initial MMI Investigator list some before, some after the awards including papers with Jen Martiny, Ed Delong, Alex Worden and Ginger Armbrust, and Mary Ann Moran.

But perhaps most relevant in terms of possible bias towards the Gordon and Betty Moore Foundation is that in 2007 my lab received funds through the MMI program for a collaborative project with Jessica Green and Katie Pollard for our “iSEEM” project on “Integrating Statistical, Ecological and Evolutionary analyses of Metagenomic Data” (see http://iseem.org) which was one of the most successful collaborations in which I have ever been involved.  This project produced something like a dozen papers and many major new developments in analyses of metagenomic data including 16S copy correction, sifting families, microbeDB, PD of metagenomes, WATERs, BioTorrents, AMPHORA. and STAP.  This project just ended but Katie Pollard and I just got additional funds from GBMF to continue related work.

So sure – I am biased.  But the program is simply great.  In the eight years since the initial grants the Gordon and Betty Moore Foundation has helped revolutionize marine microbiology.  And a lot of this came from the Investigator program and it’s emphasis on people not projects.  I note – the Moore Foundation has clearly decided that this “people not projects” concept is a good one.  A few years ago they partnered with HHMI to launch a Plant Sciences Investigator Program  which I wrote about here.

It was thus with great excitement that I saw the call for applications for the second round of the MMI Investigator program.  I certainly pondered applying.  But for many reasons I decided not to.  And today the winners of this competition have been announced and, well, it is an very impressive crew:

Some of the same crowd as the previous round.  Some new people.  Some people not there from the previous round.  All of them are rock stars in their areas especially if one takes into account how senior they are (the more junior people are stars in development).  And all have done groundbreaking work in various areas relating to marine microbiology.  The organisms covered here run the gamut including viruses, bacteria, archaea, and microbial eukaryotes.  The areas of focus covered range from biogeochemistry to ecosystem modeling with everything in between.  It really is an impressive group. Delong pioneered metagenomics and helped launch studies of uncultured microbes in the oceans.  Karl has led the Hawaii Ocean Time series and done other brilliant work.  Sullivan and Rohwer and pushing the frontiers of viral studies in the oceans.  Allen, Armbrust, and Worden are among the leaders in genomic studies of microbial eukaryotes in the marine environment.   Dubilier, Bidle, Fuhrman and Follows Stocker (double listed Follows in original post …) – though they focus on very different aspects of marine microbes – are helping lead the charge in understanding interactions across the domains of life in the marine environment.  Orphan, Saito, Deutsch, Follows and Pearson are on the cutting edge of biogeochemical studies and trying to link experimental studies of microbes to biogeochemistry of oceans.

The great thing about the “people not projects” concept is that the people funded here get to follow their own path.  They are not going to be constrained by the complications and sometime idiocy of the grant review process.  They in essence get to do whatever they want.  Freedom to follow their noses.  Or their guts.  Or whatever.  It is a refreshing concept and as mentioned above has been revolutionary in various areas of science.  There has been a slow but steady spread of the “people not projects” concept to various federal agencies too but it seems to be more of a private foundation type of strategy.  Federal Agencies are so risk averse in funding that this type of concept does not work well there.  I wish there was more.  But I am at least thankful for what HHMI and GBMF and Wellcome and Sloan and other private groups are doing in this regard.  Now – sure – all of these private foundations do not do everything perfectly.  They have blunders here and there like everyone else.  But without a doubt I think we need more of the People not Projects concept.
Oh – and another good thing.  GBMF is quite a big supporter of Open Science in it’s various guises.  So one can expect much of the data, software, and papers from their funding to be widely and openly available.   
It is a grand time to be doing microbiology largely due to revolutions in technology and also to changes in the way we view microbes on the planet.  It is an even grander time to be doing marine microbiology due to the dedication of the Gordon and Betty Moore Foundation to this important topic.  
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Get to know Jack & the story behind the paper by @gilbertjacka "Defining seasonal marine microbial community dynamics"

ResearchBlogging.org A few days ago I became aware of the publication of a cool new paper: “Defining seasonal marine microbial community dynamics” by Jack A. Gilbert, Joshua A Steele, J Gregory Caporaso, Lars Steinbrück, Jens Reeder, Ben Temperton, Susan Huse, Alice C McHardy, Rob Knight, Ian Joint, Paul Somerfield, Jed A Fuhrman and Dawn Field.  The paper was published in the ISME Journal and is freely available using the ISME Open option. If you want to know more about Jack (in case you don’t know Jack, or don’t know jack about Jack) check out some of his rantings material on the web like his Google Scholar page, and his twitter feed, his LinkedIn page, his U. Chicago page. But rather than tell you about Jack or the paper, I thought I would send some questions to the first author, Jack Gilbert and see if I could get some of the “story behind the paper” out of him.  Since Jack likes to talk (and email and do things on the web), I figured it was highly likely I could get some good answers.  And indeed I was right. Here are his answers to my quickly written up questions (been out of the office due to family illness)


1. Can you provide some detail about the history of the project … How did it start ? What were the original plans ? (not this much sequencing I am sure)

The Western English Channel has been studied for over 100 years, and is in fact it is the longest studied marine site in the world. It is the home, essentially of the Marine Biological Association, and has a long history. The idea to start contextualizing the abundant metadata (www.westernchannelobservatory.org) was started in 2003 by Ian Joint, a senior researcher at Plymouth Marine Laboratory (www.pml.ac.uk), who saw the benefit of collecting microbial life on filters and storing these at -80C. It was his vision to create and maintain this collection that enabled us to go back through this frozen time series and explore microbial life. I started working for PML in 2005, and basically was charged with trying to identify a potential technique to characterize the microbial life in these samples. initially we got funding through the International Census of Marine Life to performed 16S rDNA V6 pyrosequencing on 12 samples. We chose 2007 as the first year, almost arbitrarily, and published that work in Environmental Microbiology in 2009 (http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02017.x/abstract). However, we had already decided to go ahead, and with help from Dawn Field (Center for Ecology and Hydrology, UK) we were able to secure funding to pyrosequence 60 further amplicon samples, essentially we did 2003-2008. We deposited all these in the ICoMM dataset (link below) and it quickly became the largest study in the series. This was also a gold standard study for the Genomic Standards Consortium’s MIMARKS checklist (http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html). We published the first analysis of these data in Nature Preceedings in 2010 (http://precedings.nature.com/documents/4406/version/1). We continued to characterize the microbial communities of the L4 sampling site in the Western English Channel by employing Metagenomic and Metatranscriptomic along side more 16S rRNA V6 pyroseqeuncing across diel and seasonal time scales throughout 2008 (the final year of the 6 year time series. This study was published in PLoS ONE also in 2010 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015545). This study also included our first analysis fo archaeal diversity in the English Channel, which was also funded through the ICoMM initiative. We owe a lot to Mitch Sogin’s group for the first attempts at data analysis for the 16S rDNA profiles. We had a lot of difficulty getting the message right for the 6-year paper that was recently published in ISME J. Basically it was an issue of sequencing data as Natural History, we were generating data catalogs, and not doing enough to characterize the ecology interactions that occurred there.  So we reached out to the community, and found research groups who could help us plug that gap. Those involved Rob Knight’s team, Alice McHardy’s team, and Jed Fuhrman’s team. We worked a lot of improving this paper, and had some valuable help from a wide selection of other researchers, including Steven Giovannoni, Doug Barlett, among many others.

The publication of this study however, is just the start. 

2. Who collected the samples? Any good field stories?

Samples were all collected by the fantastic boat staff at Plymouth Marine Laboratory, who routinely go out every Monday morning to collect water and specific samples for the whole laboratory. They were the life blood of that organization. One specific I always like to relate is that during the 2008 sampling season which generated samples for both the new ISME J paper (http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2011107a.html) and the 2010 PLoS ONE paper (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015545), we wanted to get diel sampling effort during the winter spring and summer. Unfortunately the only time I could convince my group to go out sampling for 24 hours was during the summer….some times science is limited by enthusiasm ;-). Also, the site is outside the Plymouth Sea Wall – which I think is still the largest concrete structure in the UK and was built in the 19th century, so taking people out to see the site (for what it was worth ;-)) meant taking them into usually very choppy water….which made people quite sick sometimes.In May 2009, J. Craig Venter and his crew came through to start the European leg of this Global Ocean Sampling expedition at L4, specificallly the Western English Channel. Together, our team at PML on our fishing boat, Plymouth Quest, and his team on-board the 100ft yacht, Sorcerer II sampled L4 and E1 (another monitoring site) in the Western English Channel. Excitingly these data form the first part of the attempt to start cataloguing the viral and Eukaryotic metagenomic and metatranscriptomic analysis of these communities. This analysis is being also further characterized using meta-metabolomics run by Carole Llewelyn at PML and Mark Viant at University of Birmingham. Increasing the multi’omic nature of these data.

3. Can you give some web links for data, people involved , etc?

  • People on the paper – not an exhaustive list of those involved….this is a huge community effort.

4. What else do you want people to know ?

We have recently started to model the English Channel from both a taxonomic and functional perspective. I have attached a presentation that has cool gifs that demonstrate this, people can email me and request the gifs if necessary. These are generated by Peter Larsen at Argonne National Laboratory.This modelling is being driven by two new tools:(1) Predicted Relative Metabolic Turnover, which uses fucntional annotations from metagenomes to create predicted metabolomes, which enable us to accurate predict the turnover (relative consumption or production) of more than 1000 metabolites in the English Channel (http://www.microbialinformaticsj.com/content/1/1/4).(2) Microbial Assemblage Prediction, which enables the prediction of the relative abundance of every bacterial taxon at any given location and time, the predictions are driven by in situ or remotely modeled environmental parameter data. We used satellite data to produce the figures above, truely BUGS FROM SPAAAAACCCCCEEEE…..This is the new paradigm – creating information and predictive models from data – no longer will metagenomics be descriptive Natural History – it is now becoming ECOLOGY. These tools will form the corner stone the Earth Microbiome Project’s (www.earthmicrobiome.org) data analytical initiative to create predictive models of microbial taxonomic community abundance structure and functional capability defined as the ability of a community to turnover metabolites.

Note – as a bit of a side story – I am disappointed in the ISME Journals “Open” option for publishing which, though it uses a creative commons license, it is a pretty narrow one that says, for example “You may not alter, transform, or build upon this work.” That is pretty limiting.  It means, for example, that the text cannot be reworded into a database of full text of papers where one uses intelligent language processing methods to play with the text.  It also means technically I probably cannot take the figures and modify them in any way to, for example, make an interesting movie using them.  Imagine if Genbank worked this way.  Imagine if you could only look at sequences but could not make alignments of them.  It is, well, not very open. So really this should be called the ISME “No charge” option or something like that since this is not “open access” to me – I think “open access” should really be reserved for material that is free of charge and free of most/all use restrictions (I prefer  the broader version of the “open access” definition described by Peter Suber.).  Sure – the fact that ISME makes some stuff available at no charge is nice.  And that they use CC licenses is good too since these are very straightforward to interpret compared to other licenses.  But their use of the no derivatives option seems silly. Anyway – nice paper.  And I hope some of the story behind the paper is useful to people.

Reference:

Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, & Field D (2011). Defining seasonal marine microbial community dynamics. The ISME journal PMID: 21850055

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–