The Ecoscope

The main current project in our lab, the Ecoscope is an ambitious effort to produce instrumentation and methods necessary for the first ever mapping capability for microbial life.  This project is developed in close collaboration with GenØk: the National Center for Biosafety, Norway.

“First ever mapping capability”?  Yes.  Certainly, there have been many efforts in the past to image the abundance and distribution of microbes, but the results of these efforts are less than flattering. To this date, we do not have the capacity to address with real geographical resolution basic questions which traditional ecologists take for granted: where are the organisms, how many are there and how are these patterns of distribution and abundance changing in space, time and phylogeny?

The Challenge: From Detection to Monitoring, to Mapping

Epidemics and pseudo-epidemics like the recent swine-flu global scare provide some of the best-endowed and most extensive efforts at detecting, and possibly mapping, the distribution of microbes causing spectacular damage directly to humans or to their domestic biological companions (animals, crop plants).  But the truth is that even these efforts fall short of producing real maps of abundance or distribution that could be comparable to the maps which form the basis for all ecological studies in larger, visible organisms such as plants and animals.

A map represents a higher level of understanding about patterns of abundance and distribution than is normally obtained for microbes, where we tend to be satisfied with lower levels of understanding represented by detection or monitoring.  For any given organism, there is an ascending hierarchy of quality in our capacity to describe its distribution or abundance:

Detecting an organism is often a very important first step with which we simply recognize the existence of an organism in a given space and time.  In macro-ecology, detection is considered a trivial stage in a study, although there are important exceptions, for example when detecting the presence of a species thought to be extinct from a habitat.  In microbial ecology, by contrast, the simple demonstration of presence/absence of an organism in a habitat can be considered of major significance.  Our laboratory is not foreign to this experience, for example when we demonstrated the presence of viral and bacterial DNA sequences within the genomic DNA of maize plants in unexpected (and undesirable) geographical locations in the Mexican state of Oaxaca.  The commotion following this simple detection study has become quite a significant historical event (note that Jason Delborne’s treatment of this event warranted him the Society for the Social Studies of Science’s prestigious David Edge Prize for 2010).

Monitoring stands as a higher step in the scale towards understanding an organism’s patterns of abundance and distribution.  Monitoring can be seen simply as a concerted and repetitive act of detection, whereby some idea can be gained about changes in the presence/absence patterns of a given organism.

Mapping, on the other hand, implies a much deeper level of understanding than monitoring or detection efforts.  Mapping could be considered simply as a quantitatively improved monitoring just as monitoring itself could be considered as a quantitatively improved detection.  Each step implies an increase of several orders of magnitude in our physical capacity to visualize the organism in question.  If detection needs can be satisfied by one instance of secure identification, monitoring requires in the order of 103-109 detections, and no reasonable map can be constructed with fewer than 1012-1015 “detection” datapoints.

The challenge for the Ecoscope is thus a relatively inane, technical, quantitative one.  But a closer look at this challenge reveals emergent properties of complexity and social relevance that would not seem evident at first glance.

See section: Dimensions and Scales in Microbial Ecology

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