Environmental Engineering Reference
In-Depth Information
compounds. Although these approaches yield useful information for our under-
standing of microbial catabolic processes, these conditions rarely mimic what
happens in natural systems containing a large number of micro-organisms, and
their mosaic genomes (Martin
1999
; Omelchenko et al.
2003
), where growth
is often limited by complex abiotic and biotic factors. Consequently, to obtain
a more complete understanding of the acquisition of new metabolic potential,
it is often better to examine enhancement of catabolism across microbial taxa in
natural soil and water systems that have been exposed to novel new compounds
over time. Moreover, catabolic expansion, defined here as the ability of micro-
organisms to gain the ability to metabolise truly novel compounds, requires
the examination of new chemical compounds that do not share structural or
chemical properties with natural ones. In this way, the increase in catabolic
ability is less likely to occur by accumulation of point mutations over time, but
rather by more rapid acquisition of new enzymes whose activities are recruited
into existing or newly created degradation pathways. Both Janssen et al.(
2005
)
and Wackett (
2004
) provide excellent reviews on the evolution of new enzymes
for the microbial degradation of novel and xenobiotic compounds, and the
reader is pointed to these reviews for more comprehensive discussions.
Catabolic expansion vs. catabolic radiation
Several fundamentally different processes can lead to enhanced metabolic
potential of micro-organisms. Micro-organisms can gain catabolic ability via
slow, random, accumulation of mutations in existing genes, leading to new
enzymatic functions (Wright
2000
), or via acquisition of new genetic determin-
ants via horizontal acquisition (Poelarends et al.
2000
). Either of these processes
I refer to as catabolic expansion (
Fig. 10.1
), the ability of a micro-organism to
expand the range of substrates that can be used for growth and/or energy.
While both systems have been shown to operate to expand microbial meta-
bolism, the later processes are likely to lead to greater metabolic versatility in
the short term and allow for selection of growth on radically new substrates.
This is likely due to the fact that greater and faster functionality can be realised
from introgression of a new gene(s) into a microbe's metabolic machinery
than can be realised from mutation-induced 'tweaking' of an extant enzyme
for broader substrate range. This is likely reflected in the discovery of a large
number of 'foreign genes' among the genome sequences of many microbes
(Berg & Kurland
2002
). Catabolic expansion that leads to enhanced metabolic
functionality in micro-organisms can occur either via the acquisition of a single
key gene encoding for an enzyme whose product 'plugs into' existing meta-
bolic machinery (Shapir et al.
2007
), or via acquisition of a whole metabolic
pathway encoded by a suite of genes encoding for the complete metabolism
of a novel substrate (van der Meer & Sentchilo
2003
). If the new pathway is
plasmid borne, the later phenomenon also frequently results in catabolic
radiation, defined here as the spread of the ability to degrade a novel
