Monday, February 04, 2013

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 ...
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 :

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

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

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

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 :

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,

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

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