This Volume presents protocols for investigating the genetic, metabolic
and ecological potential and functional analysis of microbial
communities. Methods are described for the creation and bioinformatic
assessment of metagenomic and metatranscriptomic libraries, and for
metaproteomic analyses, which provide important insights into the
metabolic potential and interactions of community members. These in turn
lead to specific hypotheses concerning the functional contributions of
individual populations in the community, which may be investigated by
the stable isotope probing approaches described in this Volume, making
it possible to identify those community members primarily responsible
for particular functions. Methods for the direct extraction of proteins
from environmental samples for sequencing and activity tests are
presented, providing a broad overview of prevailing metabolic activities
and of the types of microbe involved in them. Protocols for the analysis
of nutrient flow through microbial communities and for the modelling of
dynamic physiological interactions in communities are also provided.
Lastly, the book presents a protocol for the quantitative assessment of
permissiveness for the transfer of conjugative plasmids, important
agents of physiological change and evolution in microbial communities.
Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of
thousands of structurally different hydrocarbons, hydrocarbon
derivatives and lipids, and a wide array of these molecules are required
for cells to function. The global hydrocarbon cycle, which is largely
driven by microorganisms, has a major impact on our environment and
climate. Microbes are responsible for cleaning up the environmental
pollution caused by the exploitation of hydrocarbon reservoirs and will
also be pivotal in reducing our reliance on fossil fuels by providing
biofuels, plastics and industrial chemicals. Gaining an understanding of
the relevant functions of the wide range of microbes that produce,
consume and modify hydrocarbons and related compounds will be key to
responding to these challenges. This comprehensive collection of current
and emerging protocols will facilitate acquisition of this understanding
and exploitation of useful activities of such microbes.
