| dc.description.abstract | By March 2015, 161 genomes of acidophilic
microorganisms had been published, including
126 permanent draft and closed genomes and 35
partial genomes reconstructed from metagenomic
data, distributed between Archaea (71), Bacteria
(86) and Eukarya (4). This provides a rich source
of latent data that can be exploited for understanding
the biology of this group of organisms
and for advancing biotechnological applications.
The genomic data are already yielding valuable
insights into the genome architecture and cellular
metabolism of acidophiles, allowing the construction
of useful models to probe their evolution and
ecophysiology both in naturally occurring acidic
environments and in industrial operations such as
in the biorecovery of metals.
Introduction
The advent of genomics and the possibility of
genome-wide comparative and evolutionary
analyses have revolutionized the field of microbiology.
This is particularly true for studies on
acidophiles where genomics have proven to be a
rich source of information that, in many cases,
has proven difficult to access via biochemical and
genetic studies given difficulties in their culturing
and manipulation.
An early review of acidophile genomes focused
on comparative genomics and provided a very
useful overview of metabolic functions and evolution
(Angelov and Liebl, 2007). Several other
mini-reviews discussed the genomics of acidophiles
but these have focused on microorganisms
involved in the biological recovery of copper and
other metals under acidic conditions (bioleaching
and biooxidation; Chapter 16) (Bonnefoy and
Holmes, 2012; Cardenas et al., 2010; Jerez, 2008;
Holmes and Bonnefoy, 2007; Quatrini et al., 2007b;
Valenzuela et al., 2006). More recent commentaries
touched upon acidophile genomics in the context
of iron oxidation (Altermann, 2014; Hedrich et al.,
2011).
The present chapter describes and updates
the genomic information discussed in the above
reviews and extends the knowledge to describe
more recently published genomes from diverse
acidic environments. The chapter does not
cover metagenomics (Chapter 13), except in the
instances where metagenomic data have been used
to partially reconstruct acidophile genomes; nor are
genomes of viruses or plasmids included (Chapter
12); also, it does not discuss functional genomic
applications such as proteomics (Chapter 14) and
transcriptomics.
One of the ultimate goals of genome science
is to predict the overall cellular organization from
molecular to higher levels, eventually leading to
useful models of interactions of microorganisms
with their environment including other microbial
co-inhabitants. This goal can be approached by
systematic comparison of genomes of related
organisms adapted to both similar and different
environments, thereby identifying corresponding
trends in genomic content. | |
