Novel statistical approach for understanding microbial community ecology

August 30, 2013
Sampling sites located ~250 m from the Columbia River in the Hanford Site 300 Area. Red circles show two-dimensional distribution of sampling locations, while the maximum horizontal distance between any two communities is ~53 m. The Hanford and Ringold formations are shown with horizontal and vertical dashes, respectively. Formation-specific analyses examine communities across the specific vertical ranges shown, whereas the "full-system" analyses include additional communities in the middle section of the Hanford formation.

To enhance the study of subsurface microbial communities underlying the U.S. Department of Energy's Hanford Site, scientists at Pacific Northwest National Laboratory developed a novel analytical framework that advances ecological understanding in two primary ways.

First, it quantitatively estimates influences of major , such as selection of the most competitive microbes, the movement of microbes through space, and chance events. Second, it uses ecological patterns to characterize measured , such as , temperature, or mineralogy, as well as the spatial pattern of unmeasured variables that select for particular microbial taxa or constrain microbe movement through the subsurface.

The , which combines a number of different statistical analyses, showed that microbial community changes in space and time are affected by multiple ecological processes, and the relative balance among processes varies across and spatial scales. The ultimate result is a conceptual model of within and between geologic formations underlying the Hanford Site's 300 Area. Further, the ecological knowledge provided by the new statistical approach far outstrips information provided by other approaches.

Spatial turnover in the composition of is governed by a combination of ecological processes, yet commonly applied statistical approaches can't quantitatively estimate the relative influences of these processes, nor can they rigorously identify environmental features that impose them.

The PNNL-developed framework is broadly applicable and can be used to make direct comparisons across spatial scales; in different ecosystems, such as terrestrial soil and surface water; and with other taxonomic groupings, such as plants and fungi. In particular, the framework will enable improved predictive modeling of spatial and temporal variation in microbial communities. Coupling the framework to biogeochemical models can lead to more precise models that better predict important processes, such as contaminant transport or the fluxes of greenhouse gases.

The framework leverages evolutionary relationships among microbial taxa and combines that information with statistical randomization approaches and spatial patterns in microbial community composition. It further characterizes the spatial structure of an unmeasured environmental variable that selects for particular microbial taxa.

Work to date in the Hanford 300 Area points to a strong influence of river water intrusion from the Columbia River on subsurface . Field efforts are currently under way to more directly evaluate the effects of river water intrusion on subsurface microbial processes. The new analytical framework will be critical for interpreting linkages among biotic and abiotic components in space and time.

In addition, metagenomic information will be exploited to extend the analytical framework beyond microbial community composition to its metabolic potential. Resulting ecological inferences will be used to develop more biologically informed, field-scale biogeochemical models that incorporate spatiotemporal predictions of the potential for biogeochemical reactions.

Explore further: Modeling microbes to manage carbon dioxide

More information: Stegen, J. et al. 2013. Quantifying Community Assembly Processes and Identifying Features That Impose Them, The ISME Journal, June 6, 2013. DOI: 10.1038/ismej.2013.93

Related Stories

Modeling microbes to manage carbon dioxide

February 7, 2012

( -- In the past decade, microbiologists began realizing that communities of microbes process energy and materials, which affects their environments. To understand how microbial communities function in a natural ...

Taking stock of subsurface microbial communities at Hanford

March 13, 2012

Taking a census provides valuable information about residents' ages, employment, makeup, living conditions, etc. Most censuses are taken door to door or by mail. But if the community lives in areas that are inaccessible by ...

Microbial changes regulate function of entire ecosystems

May 31, 2013

A major question in ecology has centered on the role of microbes in regulating ecosystem function. Now, in research published ahead of print in the journal Applied and Environmental Microbiology, Brajesh Singh of the University ...

Recommended for you

A better way to read the genome

October 9, 2015

UConn researchers have sequenced the RNA of the most complicated gene known in nature, using a hand-held sequencer no bigger than a cell phone.

Threat posed by 'pollen thief' bees uncovered

October 9, 2015

A new University of Stirling study has uncovered the secrets of 'pollen thief' bees - which take pollen from flowers but fail to act as effective pollinators - and the threat they pose to certain plant species.

Most EU nations seek to bar GM crops

October 4, 2015

Nineteen of the 28 EU member states have applied to keep genetically modified crops out of all or part of their territory, the bloc's executive arm said Sunday, the deadline for opting out of new European legislation on GM ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.