Metadata to collect while collecting plant associated microbial samples in the field

Another question for Twitter with some answers by Storify. Not I am putting in below the fold here so that the Storify emded only launches for those who want it to …
//storify.com/phylogenomics/metadata-to-collect-while-collecting-plant-associa.js[View the story “Metadata to collect while collecting plant associated microbial samples in the field” on Storify] In addition Russell Neches in my lab would like to add the following comments, which were too long for the comment option here.

The most important thing for interpreting -omic data is context. For
genomic data, this mostly means compare and contrast analysis against
other genomes, although there are other tools (GWAS-type studies,
ChIP-seq/chip, footprinting…). For metagenomes, comparisons against
other similar metagenomes can be of limited utility if the taxa
represented do not overlap very much.

The easiest thing would be to bring a smart phone and log GPS

coordinates and take wide and closeup photos, and make absolutely sure

that each one is explained in the field notes. This doesn’t necessarily
provide quantitative information, but it’s *REALLY* helpful to anyone

trying to analyze the data who wasn’t on the field mission. And it’s
cheap and easy.

For quantitative metadata, there are usually a number of abiotic
parameters that drive community structure, and many of these are
relatively easy to instrument. For example, pH, temperature and moisture
are very strongly correlated with community structure in terrestrial
soils. These parameters are very easy to measure. There are of course
other parameters that might be interesting; CO2, CO, CH4, C2H5OH, O2,
N2, nitrate, nitrite, phosphorous… but these are somewhat more
difficult to instrument at the moment, and (as far as I know) are
usually not as correlated with the very broad impact of pH, temperature
and moisture unless the system is near an extreme (e.g., the whole
system goes anaerobic, or metal-starvation in the open ocean).

However, while these parameters are easy to measure, they can also
fluctuate on time-scales that are relevant to microbial growth. As a
result, the temporal (and perhaps spacial) variation of these parameters
may be more important to the community structure than their “typical”
values. In way that is tends to frustrate field mission planning, it is
the temporal fluctuations *PRIOR* to sampling that are relevant.

There are two approaches : telemetry and local assistance. Telemetry
(“measurement from afar”) means placing instrumentation at the site that
has the ability to log or transmit data. Local assistance would vary
depending on the context of the site, but basically amounts to
partnering with someone who actually lives near the study site and
somehow convincing them to take measurements for you. Of course, the two
approaches are not mutually exclusive.

The simplest and probably best approach would be to partner with someone
near the study site who teaches fourth grade. Send them enough simple
gardener’s soil chemistry meters for their class (plus some extra for
the ones that inevitably get lost, disassembled or turned into
implements of mayhem and destruction).

For example, a quick search on Amazon turns up dozens of fairly
inexpensive gardening tools for measuring pH, moisture, temperature and
light intensity. Here’s one that looks like it might be useful :

http://www.amazon.com/Digital-Soil-Light-Tester-Plants/dp/B000RN23DM/

Here’s an even cheaper one that does pH, moisture and light, doesn’t
need a battery, and costs less than seven bucks :

http://www.amazon.com/Moisture-Meter-Light-Test-Function/dp/B007FMVOVK/

If you were asking a class of fourth graders to help gather metadata for
you, using instruments like these would cost perhaps $300, including
instruments, stationary, surveying flags, etc. Make that $500, and send
lots of extra stationary. Fourth grade classrooms never have enough
stationary.

Of course, if you’re going to ask people to do work for you, you must
treat them accordingly. Taking careful, regular measurements and writing
them down in a notebook is the bread-and-butter of science, and people
who do this work are called “scientists,” not “helpers.” There are
myriad implications to this, but one that I hope more people will
consider is sharing authorship. It is fair, it is honest, and it is
inexpensive.

The other option is telemetry. Thanks in no small part to the Arudino
project, this has gotten vastly easier and cheaper. At the cost of
learning a little bit about soldering and digital logic, you can wire up
virtually any sensor you like to a microcontroller, and then push that
data over a variety of communications platforms. There are Arduino
shields that interface with Ethernet, Wifi, Bluetooth, GSM, and even
satellite networks. Even a satellite uplink interface can be hacked
together for less than $200.

Of course, there are a lot of people interested in telemetry of various
sorts, and so you can find Arduino derivatives that have a lot of the
work done for you. For example, if you happen to want to want pH
telemetry, and your site happens to be within a few dozen meters of
someplace you can safely leave an old laptop, this product might
interest you :

http://www.sparkyswidgets.com/Products/Store/Details/tabid/81/ProductID/4/Default.aspx

Here’s another Arduino variant with an onboard FLASH logging interface,
solar/LiPo power management, a real time clock, a temperature sensor,
and interfaces for standard Arduino shields (e.g., a GSM shield), and an
interface for Xbee-style boards (e.g., bluetooth, Xbee, GPS, FM radio,
Wifi).

http://www.seeedstudio.com/wiki/Seeeduino_Stalker_v2.3

Attach sensors. Write software. Add battery and solar panel. Put into
watertight box. Deposit at field site.

Very nice new #PLoSGenetics paper on "Functional Phylogenomics" of Seed Plants

Update2 – 12/22 – Data available here.  Thanks to the authors for clearing things up quickly.


Update1 –  12/19 – Data for this paper seems to be unavailable – not sure why – but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there.  Note – this is one reason that all data sets should be made available at the journal or third party sites.


Original post:

OK never mind that the terminology of “functional phylogenomics” is a tiny bit vexing to me (long story – some other time perhaps). The paper behind it – PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.

Here’s what the authors did (a very coarse summary)

1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)

2. Constructed a “total evidence” phylogeny for these taxa (using a few approaches) 

3. Use this phylogeny to reinterpret some general features of the evolution of plants 
4. Searched for gene ontology categories (in annotated genes from these organisms) that agreed with the phylogeny. In essence, this seems to be a search for shared-derived traits (i.e., synapomorphies) in particular clades. 
5. Generated hypothesis about functional evolution in particular clades.
Overall, there is a lot that is really fascinating in here and this approach seems very powerful (though I note – I think something akin to this though not as comprehensive or as careful has been done for other groups but not sure).  Check out the paper for more detail …
Lee EK, Cibrian-Jaramillo A, Kolokotronis S-O, Katari MS, Stamatakis A, et al. (2011) A Functional Phylogenomic View of the Seed Plants. PLoS Genet 7(12): e1002411. doi:10.1371/journal.pgen.1002411

A great moment for plant sciences: winners of HHMI-GBMF competition for Plant Science Program Investigators announced

This is truly the golden era for plant sciences. One key sign of this is the announcement of the winners of the competition to become HHMI Investigators in Plant Sciences.
HHMI, the Howard Hughes Medical Institute, has for many years picked HHMI Investigators in Biomedical Research. Those picked get guaranteed funds for 5 years and become technically employees of HHMI in order to get them out of miscellaneous burdensome university activities. It’s a win win situation for universities because HHMI pays for space and salaries for the Investigators. I myself tried to get me one of these “Uncle Howie” types of positions a few years ago but did not win out. My brother, Michael, did. The other people they picked the year they picked Michael and not me were all very good, so I actually did not feel so bad about not getting it.
HHMI has also invested in other areas related to biomedical research including funding Janelia Farm, and Early Career Scientist program, as well as many educational activities.
The GBMF, aka the Gordon and Betty Moore Foundation has itself made major contributions to science and medicine in various ways. One example is the Marine Microbiology Initiative (MMI) (which funded the iSEEM project for which I am PI) and cool work out of many top marine labs. In fact, the MMI program did something rarely seen outside of HHMI – they funded “people not projects” by creating MMI Investigators who got a good chunk of money to do pretty much whatever they wanted.
Thus it was great to hear some time ago that GBMF and HHMI were coming together to create a Plant Sciences Investigator program. I confess even though I am not a real plant biologist I considered applying for this because I have shifted much of my work recently into studies of plant associated microbiomes. But I did not apply. And I kept wondering – who would emerge from the competition as winners. Would they be people I respected/had heard of?
Well the wait is over. Last week the winners were announced: HHMI News: 2011 Plant Science Program HHMI-GBMF Investigators. And it is quite an incredible crew. The press release from HHMI-GBMF is quite useful (unlike many press releases in the sciences). Here is a list of the winners with some additional details (taken from the HHMI site – I hope they do not mind).










JUNE 16, 2011
2011 Plant Science Program 
HHMI-GBMF Investigators

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Philip Benfey, Ph.D.
Philip Benfey, Ph.D.
Duke University
Durham, NC

Benfey is studying how plants control the form and function of their root systems. Moresmall arrow
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Dominique Bergmann, Ph.D.
Dominique Bergmann, Ph.D.
Stanford University
Palo Alto, CA

By studying the formation of the structures plants use to control the exchange of water and carbon dioxide, Bergmann is making fundamental discoveries about how cells acquire their fates and establish the patterns needed to build a complete organism. Moresmall arrow
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Simon Chan, Ph.D.
Simon Chan, Ph.D.
University of California, Davis
Davis, CA

By studying basic chromosome biology, Chan has made discoveries that have practical implications for making crop plants easier to breed. Moresmall arrow
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Xuemei Chen, Ph.D.
Xuemei Chen, Ph.D.
University of California, Riverside
Riverside, CA

Chen’s lab has two overlapping goals: deciphering the molecular programs that control flower formation, and determining how small RNAs control gene activity in plants. Moresmall arrow
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Jeff Dangl, Ph.D.
Jeff Dangl, Ph.D.
University of North Carolina at Chapel Hill
Chapel Hill, NC

Plants are confronted by a daunting range of bacteria, fungi, and viruses. Dangl is working to understand how plants recognize beneficial versus pathogenic microbes. Moresmall arrow
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Xinnian Dong, Ph.D.
Xinnian Dong, Ph.D.
Duke University
Durham, NC

Dong is investigating how plant defense genes promote resistance to pathogens. Moresmall arrow
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Jorge Dubcovsky, Ph.D.
Jorge Dubcovsky, Ph.D.
University of California, Davis
Davis, CA

Dubcovsky’s investigations of wheat genetics have enabled him to boost the plant’s nutritional content, increase yield, and optimize the growing cycle for particular climates. Moresmall arrow
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Joseph Ecker, Ph.D.
Joseph Ecker, Ph.D.
Salk Institute for Biological Studies
La Jolla, CA

Ecker is trying to understand how plants perceive and respond to gases required for stress protection, seed germination and fruit ripening. Moresmall arrow
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Mark Estelle, Ph.D.
Mark Estelle, Ph.D.
University of California, San Diego
La Jolla, CA

Estelle is investigating how hormones help plants respond to alter their growth in response to changes in including light, temperature, water, and nutrient availability. Moresmall arrow
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Sheng Yang He, Ph.D.
Sheng Yang He, Ph.D.
Michigan State University
East Lansing, MI

He works to identify the techniques that bacteria use to attack plants and make them more susceptible to disease, which has implications for both crops and human health. Moresmall arrow
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Robert Martienssen, Ph.D.
Robert Martienssen, Ph.D.
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY

The gene silencing methods studied in Martienssen’s lab keep mobile genetic elements under control and are critical to normal plant reproduction and development. Moresmall arrow
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Elliot Meyerowitz, Ph.D.
Elliot Meyerowitz, Ph.D.
California Institute of Technology
Pasadena, CA

One of the questions that interests Meyerowitz is how plant cells recognize and respond to chemical and mechanical signals. Moresmall arrow
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Krishna Niyogi, Ph.D.
Krishna Niyogi, Ph.D.
University of California, Berkeley
Berkeley, CA

Niyogi has spent two decades delving into photosynthesis and has made fundamental discoveries that help scientists understand the strategies plants use to adapt to their environment. Moresmall arrow
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Craig Pikaard, Ph.D.
Craig Pikaard, Ph.D.
Indiana University at Bloomington
Bloomington, IN

One of the major research interests in Pikaard’s lab is understanding how plant genes are silenced. Moresmall arrow
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Keiko Torii, Ph.D.
Keiko Torii, Ph.D.
University of Washington
Seattle, WA

Torii’s lab studies how plant cells coordinate proliferation and differentiation during organ morphogenesis to generate beautiful, orderly patterns. Moresmall arrow

It is a phenomenal crew. I know many of them personally and professionally and there is no doubt they are among the most creative and productive in life sciences, let alone in plant biology. Philip Benfey at Duke has been involved in this massive DARPA project in which I have also been involved on the “Fundamental Laws of Biology” and he in part is what inspired me to get more into plant – microbe interaction studies. I have known Jeff Dangl at UNC for many years and in addition to always being impressed with his science his recent shift to working on “microbiomes” of plant roots has inspired me to do more experiments in model genetic hosts. This is part of why my lab is now involved in studies of microbes associated with rice and corn. I have also known Joe Ecker for many years too (I worked on the Arabidopsis thaliana genome sequencing paper in which he was involved) and every time I see him I end up wanting to do another plant associated project. And I have seen him and Jeff Dangl a lot since they have both been outside advisors to a variety of DOE-JGI projects in which I am involved.  I worked with Elliot Meyerowitz on a National Academy of Science panel that came out with a report on the future of the life science “The New Biology for the 21st Century”.  Elliot was a steadfast defender of basic science and small scale science in that panel.  I interacted with Craig Pikaard many years ago regarding the finding of a novel RNA polymerase homolog (RNA pol IV) in the Arabidopsis genome.   I could go on and on but won’t. Suffice it to say, I am very impressed with the collection of people that are the winners of the competition.
I will however go on and on a bit about one other thing. Two of the winners are from UC Davis: Simon Chan and Jorge Dubcovsky. Both are phenomenal and great to have on campus. In fact, Davis is one of only two places that has two winners. Duke is the other one. UCSD sort of has two if you include Joe Ecker from Salk which is around the corner. This makes me proud to be at UC Davis which is a hotbed for good plant biology research.
Anyway, I think it is great that both HHMI and GBMF are getting more into plant sciences – especially now that federal funding programs are hurting a bit.

As a last little bit here, here are some fully open access papers by this crew:

There are many many more – yet another thing I like about this group. 

Long’s Drug’s Plant Graveyard

I went to Long’s today on Covell to drop off and then pick up a prescription. In the time I was waiting I decided to check out their “Garden Center.” I was just curious and did not have high expectations when I went in. Well, I can say without a doubt that I was underwhelmed. It was more like a plant graveyard than a Garden Center. There were multple dead trees in pots there, some of which were not even upright anymore. And many of the perennials seemed dead too. It looked like nobody had even been in there in weeks. You would think at some point they would reduce their prices to try and sell stuff before it died but apparently not – the prices were nothing special even on the nearly dead stuff.

I have been checking out the various nurseries and garden cente’s in the area looking for a few things to jazz up the yard. Ace Hardware is OK but I almost never end up getting anything there despite browsing for a while. Redwood Barn on the other hand, is a dream come true. We just bought a lovely tree there – not too expensive – but that is beside the point. Most importantly, the workers there know their stuff and spent the time with me to discuss what type of tree we wanted and they came up with 4-5 suggestions. Perhpas Long’s shold ditch their Garden Center or maybe just let it grow wild.