Agriculture Reference
In-Depth Information
Ecology of Soil Microbes
Cultivation and Characterization of Ecologically Relevant Microbes
While molecular surveys are helping to delineate the distribution and temporal
dynamics of microbes in the environment, understanding the ecology of microbes
requires studying the functions of the entire organism, not just its DNA sequences.
Culture-based approaches—in which individual strains or consortia of microbes
are isolated and grown—provide the most information about life history traits of
microbes that thrive in the soil environment. Life history traits are characteristics
that influence the growth, reproduction, or survival of an organism. Few studies of
microbes embrace the notion of life histories, perhaps because they do not have
obvious counterparts to plant or animal life history traits such as clutch size or
parental care. Since natural selection favors individuals who are best able to survive
and leave viable progeny regardless of whether they are single- or multicellular, the
study of life history traits in microbes should be as useful as it has been in plants
and animals and can provide a common currency to compare ecological strategies.
Microbiologists have traditionally used media that contain abundant organic
compounds and other nutrients to grow and study microbes. These “rich” media
formulations select for copiotrophic microbes—organisms that capitalize on the
availability of abundant resources and grow quickly. Cultivating oligotrophs—
organisms that thrive in resource-poor environments—requires a different strategy.
Key culturing elements are growth media with limited nutrients, atmospheres with
less than ambient O
2
concentrations, and sufficient time for slow-growing colo-
nies to form (e.g., Janssen et al. 2002, Stevenson et al. 2004). This approach has
enabled many never or rarely cultured bacteria to be grown in the lab, including
representatives of the abundant but poorly characterized phyla Acidobacteria and
Verrucomicrobia.
Acidobacteria are present in soils worldwide (Janssen 2006) and abundant in
many KBS LTER soils, as noted earlier, yet few cultivated representatives of this
cosmopolitan phylogenetic group exist. Presumably, they are unable to compete
with the fast-growing bacteria that prosper on the rich media commonly used
in microbiology laboratories. To learn more about the metabolic properties and
potential ecological roles of members of this phylum, Eichorst et al. (2007) iso-
lated Acidobacteria strains from KBS LTER soils using incubation conditions
and media designed to mimic their natural environment. Cultivation conditions
included low concentrations of nutrients, plant polymers as sole C and energy
sources, and extended (3 to 4-week) incubation periods. Altered incubation atmo-
spheres with decreased concentrations of O
2
and elevated levels of CO
2
resulted in
a slightly acidified medium with a pH similar to
in-situ
measurements of soil pH
at KBS LTER.
When plant polymers were used as a C and energy source, the diversity of
Acidobacteria growing in culture increased relative to those cultured on simple
sugars (Eichorst et al. 2011). All the cultivated strains of Acidobacteria contained
either one or two copies of the 16S ribosomal RNA-encoding gene that, along with
