Agriculture Reference
In-Depth Information
2015, Paul et al. 2015, Millar and Robertson 2015; Chapters 1, 5, and 9 in this
volume). Of particular interest is the partitioning of C and N between bioavail-
able compounds in the soil and the exchange of greenhouse gases between soils
and the atmosphere. These processes are heavily influenced by microbial activity,
so it is possible that altered partitioning of C and N could result from changes in
the microbial community that are generated by different land uses and manage-
ment practices. The first step to understanding potential relationships between soil
microbes and the production and consumption of greenhouse gases is to determine
the structure of microbial communities in different soils.
We begin this chapter with an overview of the composition of microbial com-
munities in soils under different land management practices. We then discuss
the relationships between subsets of these communities and the fluxes of meth-
ane (CH
4
), nitrous oxide (N
2
O), and carbon dioxide (CO
2
)—the three greenhouse
gases that contribute most to climate change (IPCC 2007). Third, we consider
the life histories of bacteria in soil and discuss how an ecological perspective has
informed new models relating microbial community structure to function. We end
the chapter with some thoughts about long-term research to test these models and
evaluate the potential for restoring ecological function by manipulating bacterial
diversity.
Microbial Diversity in Soil
Molecular Surveys
As in the majority of complex microbial communities in nature, most microbes
in soil have yet to be cultured in the laboratory: fewer than 1% of the microbes
that can be visualized microscopically grow under traditional cultivation conditions
(Staley and Konopka 1985). Cultivated strains provide valuable insights into the
metabolism and behavior of microbes from soil (discussed below), but the compo-
sition of microbial communities can be determined more rapidly and comprehen-
sively through the characterization of extracted nucleic acids without cultivation.
Research at KBS LTER has used some of the most common strategies for these
molecular surveys (Fig. 6.1).
The key to comparing these complex microbial communities is obtaining DNA
sequences of conserved genes. The nucleotide sequence of a conserved gene is sim-
ilar in all members because the encoded function of the gene is retained. However,
certain nucleotides can be substituted for others without disrupting the gene func-
tion. Over time these changes accumulate, so organisms can be grouped according
to the location and number of substitutions in their sequences, with the closest
relatives having fewest differences. To provide enough material for sequencing, the
target gene in an environmental sample must be amplified from each microbe, typi-
cally by the process of Polymerase Chain Reaction (PCR). Surveys are often based
on comparative analyses of the gene encoding the small subunit ribosomal RNA
(SSU rRNA), which has a sedimentation coefficient of 16S in bacteria and Archaea
and 18S in eukaryotes.
