Download Exploration of Antarctic Subglacial Aquatic Environments: Environmental and Scientific Stewardship PDF

TitleExploration of Antarctic Subglacial Aquatic Environments: Environmental and Scientific Stewardship
Author
LanguageEnglish
File Size4.2 MB
Total Pages163
Document Text Contents
Page 2

Committee on Principles of Environmental Stewardship for the
Exploration and Study of Subglacial Environments

Polar Research Board

Division of Earth and Life Studies

THE NATIONAL ACADEMIES PRESS
Washington, D.C.
www.nap.edu

Page 81

�0 EXPLORATION OF ANTARCTIC SUBGLACIAL AQUATIC ENVIRONMENTS

BOX 3.2
Bacterial Speciation Processes

The definition of a bacterial species remains an elusive concept in microbiology in large part
due to the fact that bacteria are clonal and reproduce asexually. As a result, the Biological Species
Concept first espoused by Ernst Mayr (1942), which broadly states that groups of actual or potentially
interbreeding natural populations can reproduce only among themselves to the exclusion of all others,
is not applicable. At present, somewhat arbitrary operational definitions based on phenotypic char-
acterizations (Bochner 1989; Mauchline and Keevil 1991) and molecular biological tools such as the
association of genomic DNA in standardized DNA/ DNA hybridizations (typically >70 percent) and/or
gene sequence identity of ≥97 percent for the16S ribosomal RNA (rRNA), are most commonly used
to define bacterial species (Wayne et al. 1987; Stackebrandt and Goebel 1994; Konstantinidis andKonstantinidis and
Tiedje 2005). The ever-increasing amount of information derived from comparative genomic analyses
is providing fundamentally new insights into the question of what constitutes a bacterial species while
further revealing that bacterial genomes are not static entities; many mechanisms or combinations
thereof can contribute to both maintenance and change of genome structure and content over time
(Ward and Fraser 2005). Among the most important forces contributing to the evolution of bacterial
species are the interplay between the rates of mutation and homologous recombination (where homo-
logous in this case denotes a substitution of some portion of a genomic sequence with a sequence
of high similarity ) and the influence of biogeography in the divergence of bacterial lineages through
adaptations and separation into ecological niches (Nesbø et al. 2006).
Genetic variations are the source upon which evolutionary forces such as genetic drift and natural
selection act. Some mutations in DNA are spontaneous, random events that can result from several
possibilities. For instance, mutations can arise by the exposure of DNA to ionizing radiation, ultraviolet
radiation, and some chemicals. Normally DNA sequences are copied precisely during replication;
however, errors in DNA replication can result in changes in gene sequence. In addition, a variety of
recombinatory processes can occur in nature that contribute to genetic variability by joining DNA from
different biological sources (Graur and Li 2000).
Basic concepts of population genetics suggest that most mutations are deleterious to the fitness
of an individual (ability of the individual to survive and reproduce) and are selected against causing
their removal from the population, a process referred to as negative or purifying selection. Mutations
can also result in alleles (alternative forms of the gene) of similar fitness that are considered neutral
mutations and are subject to loss from or fixation within a population as a result of stochastic forces.
Occasionally, a mutation may produce an allele that increases the fitness of an individual. These
advantageous mutations will be subjected to positive selection and will tend to be fixed more rapidly
in a population than to neutral mutations (Graur and Li 2000).

Homologous recombination is recognized as a vital process to maintain chromosome integrity by
facilitating the repair of damaged DNA that is mediated largely through pathways controlled by the
enzyme RecA (Ivanic-Bacce et al. 2006). However, homologous recombination is also increasingly
being recognized as central to the creation of genetic variability and as an important force in genome
change within and between prokaryotic lineages (Fraser et al. 2007). Within prokaryotic lineages,
sources of change can result from rearrangement, duplication, or loss of chromosomal segments dur-
ing DNA replication. Further recombination facilitates the exchange of DNA between lineages from a
donor to a recipient, a process referred to as horizontal or lateral gene transfer (Ochman et al. 2000).
Among the best-identified mechanisms of lateral gene transfer are those of transformation, conjuga-
tion, and transduction. Conjugation and transduction require an intermediary to genetic exchange, a
plasmid in the case of conjugation and a bacteriophage or bacterial virus in the case of transduction.
Alternatively, transformation, the third mechanism, involves the uptake of free DNA from the environ-
ment (Graur and Li 2000). Recombination is not restricted to the transfer of homologous DNA from
a donor to a recipient in bacteria. One possible result of recombinatorial events is the integration of
heterologous DNA from the donor to the recipient along with flanking homologous DNA. Therefore,
under some circumstances DNA from distantly related lineages can also be transferred. Additional
mechanisms that can facilitate this type of integration include transposable elements, such as inser-
tion sequences, transposons, and retroelements (Bennet 2004). Site-specific recombination systems
such as integrons (reviewed in Mazel 2006) have also been recognized as important mobile elements
in acquiring exogenous genes and shaping genome change.
In mammalian reproduction, recombination accompanies each reproductive event. The rate of
recombination in bacteria does not approach this frequency (Levin and Bergstrom 2000). However, it
is possible that bacterial recombination can exceed mutation as a source of genetic variability, rais-
ing the possibility that at least a modified form of the Biological Species Concept may be applicable
to some bacteria under certain circumstances. For example, related bacterial lineages may share a
core set of genes via recombination in a common gene pool (Doolittle and Papke 2006).
At present there are a number of competing ideas concerning how mechanisms that foster genetic
variability and the forces of evolution interact to both maintain sufficient genetic similarity (effectively
preserving species) and to create genetic divergence between species. Currently an intense debate
reigns as to the relative importance of barriers to genetic exchange by homologous recombination,
which is broadly captured by two models: “the bacterial species model” (Doolittle and Papke 2006;
Nesbø et. al 2006) versus natural selection of adaptive mutants that use similar resources and inhabitø et. al 2006) versus natural selection of adaptive mutants that use similar resources and inhabit et. al 2006) versus natural selection of adaptive mutants that use similar resources and inhabit
similar physical locations (“the ecotype model”) (Cohan 2002). As the search proceeds, to unlock the
underlying principles that define a bacterial species will require the continued integration of results
from diverse areas of biology. The exploration of subglacial aquatic environments will provide a unique
lens through which to view and study these questions.

ice sheet originated from the islands and continents of the temperate latitudes of the
Southern Hemisphere.”

EVOLUTION OF LIFE IN SUBGLACIAL AQUATIC ENVIRONMENTS

Antarctic subglacial aquatic environments represent potentially rich and largely
unexplored storehouses of genetic information. As such, a variety of biogeochemical
processes could potentially be at work, resulting in unique metabolically active micro-
bial assemblages in terms of structure and function. The age of the oldest ice in the
ice sheet is 1 million years (EPICA 2004; Peplow 2006), and this has been taken to
indicate the length of time of microbial isolation of Lake Vostok. Although 1 million
years is not a considerable amount in terms of prokaryotic evolution, some changes

Page 82

SUBGLACIAL ENVIRONMENTS: BIOLOGICAL FEATURES ��

may have occurred to help these organisms adapt to the cold, dark, oligotrophic envi-
ronment (Tiedje 1989).

The waters of Lake Vostok have been isolated from direct atmospheric contact
for at least 15 million years (Christner et al. 2006), giving a much longer time for
evolutionary processes to operate (Box 3.3), and the founding populations in the lake
may even be older if the original microbiota were derived from Antarctic bedrock or
sediments. Then they could have been isolated from the surface microbial populations
prior to the formation of Lake Vostok, as much as 35 million to 40 million years ago
(Tiedje 1999).

As discussed by Tiedje (1999), studies on the rate of genetic change of microbes
in nature indicate that speciation could take 10 million to 100 million years. An often
cited estimate of speciation is the divergence of Escherichia coli and Salmonella enterica

BOX 3.2
Bacterial Speciation Processes

The definition of a bacterial species remains an elusive concept in microbiology in large part
due to the fact that bacteria are clonal and reproduce asexually. As a result, the Biological Species
Concept first espoused by Ernst Mayr (1942), which broadly states that groups of actual or potentially
interbreeding natural populations can reproduce only among themselves to the exclusion of all others,
is not applicable. At present, somewhat arbitrary operational definitions based on phenotypic char-
acterizations (Bochner 1989; Mauchline and Keevil 1991) and molecular biological tools such as the
association of genomic DNA in standardized DNA/ DNA hybridizations (typically >70 percent) and/or
gene sequence identity of ≥97 percent for the16S ribosomal RNA (rRNA), are most commonly used
to define bacterial species (Wayne et al. 1987; Stackebrandt and Goebel 1994; Konstantinidis andKonstantinidis and
Tiedje 2005). The ever-increasing amount of information derived from comparative genomic analyses
is providing fundamentally new insights into the question of what constitutes a bacterial species while
further revealing that bacterial genomes are not static entities; many mechanisms or combinations
thereof can contribute to both maintenance and change of genome structure and content over time
(Ward and Fraser 2005). Among the most important forces contributing to the evolution of bacterial
species are the interplay between the rates of mutation and homologous recombination (where homo-
logous in this case denotes a substitution of some portion of a genomic sequence with a sequence
of high similarity ) and the influence of biogeography in the divergence of bacterial lineages through
adaptations and separation into ecological niches (Nesbø et al. 2006).
Genetic variations are the source upon which evolutionary forces such as genetic drift and natural
selection act. Some mutations in DNA are spontaneous, random events that can result from several
possibilities. For instance, mutations can arise by the exposure of DNA to ionizing radiation, ultraviolet
radiation, and some chemicals. Normally DNA sequences are copied precisely during replication;
however, errors in DNA replication can result in changes in gene sequence. In addition, a variety of
recombinatory processes can occur in nature that contribute to genetic variability by joining DNA from
different biological sources (Graur and Li 2000).
Basic concepts of population genetics suggest that most mutations are deleterious to the fitness
of an individual (ability of the individual to survive and reproduce) and are selected against causing
their removal from the population, a process referred to as negative or purifying selection. Mutations
can also result in alleles (alternative forms of the gene) of similar fitness that are considered neutral
mutations and are subject to loss from or fixation within a population as a result of stochastic forces.
Occasionally, a mutation may produce an allele that increases the fitness of an individual. These
advantageous mutations will be subjected to positive selection and will tend to be fixed more rapidly
in a population than to neutral mutations (Graur and Li 2000).

Homologous recombination is recognized as a vital process to maintain chromosome integrity by
facilitating the repair of damaged DNA that is mediated largely through pathways controlled by the
enzyme RecA (Ivanic-Bacce et al. 2006). However, homologous recombination is also increasingly
being recognized as central to the creation of genetic variability and as an important force in genome
change within and between prokaryotic lineages (Fraser et al. 2007). Within prokaryotic lineages,
sources of change can result from rearrangement, duplication, or loss of chromosomal segments dur-
ing DNA replication. Further recombination facilitates the exchange of DNA between lineages from a
donor to a recipient, a process referred to as horizontal or lateral gene transfer (Ochman et al. 2000).
Among the best-identified mechanisms of lateral gene transfer are those of transformation, conjuga-
tion, and transduction. Conjugation and transduction require an intermediary to genetic exchange, a
plasmid in the case of conjugation and a bacteriophage or bacterial virus in the case of transduction.
Alternatively, transformation, the third mechanism, involves the uptake of free DNA from the environ-
ment (Graur and Li 2000). Recombination is not restricted to the transfer of homologous DNA from
a donor to a recipient in bacteria. One possible result of recombinatorial events is the integration of
heterologous DNA from the donor to the recipient along with flanking homologous DNA. Therefore,
under some circumstances DNA from distantly related lineages can also be transferred. Additional
mechanisms that can facilitate this type of integration include transposable elements, such as inser-
tion sequences, transposons, and retroelements (Bennet 2004). Site-specific recombination systems
such as integrons (reviewed in Mazel 2006) have also been recognized as important mobile elements
in acquiring exogenous genes and shaping genome change.
In mammalian reproduction, recombination accompanies each reproductive event. The rate of
recombination in bacteria does not approach this frequency (Levin and Bergstrom 2000). However, it
is possible that bacterial recombination can exceed mutation as a source of genetic variability, rais-
ing the possibility that at least a modified form of the Biological Species Concept may be applicable
to some bacteria under certain circumstances. For example, related bacterial lineages may share a
core set of genes via recombination in a common gene pool (Doolittle and Papke 2006).
At present there are a number of competing ideas concerning how mechanisms that foster genetic
variability and the forces of evolution interact to both maintain sufficient genetic similarity (effectively
preserving species) and to create genetic divergence between species. Currently an intense debate
reigns as to the relative importance of barriers to genetic exchange by homologous recombination,
which is broadly captured by two models: “the bacterial species model” (Doolittle and Papke 2006;
Nesbø et. al 2006) versus natural selection of adaptive mutants that use similar resources and inhabitø et. al 2006) versus natural selection of adaptive mutants that use similar resources and inhabit et. al 2006) versus natural selection of adaptive mutants that use similar resources and inhabit
similar physical locations (“the ecotype model”) (Cohan 2002). As the search proceeds, to unlock the
underlying principles that define a bacterial species will require the continued integration of results
from diverse areas of biology. The exploration of subglacial aquatic environments will provide a unique
lens through which to view and study these questions.

Page 162

APPENDIX C ���

EAIS East Antarctic Ice Sheet
EPICA European Project for Ice Coring in Antarctica

FISH Fluorescence In Situ Hybridization
FOSA Heptadecafluorooctane Sulfonamide

GC-MS Gas Chromatography-Mass Spectroscopy
GISP Greenland Ice Sheet Project
GRIP Greenland Ice Core Project

HCFC Hydrochlorofluorocarbon

ICSU International Council for Science
IEE Initial Environmental Evaluation
IGY International Geophysical Year
IODP Integrated Ocean Drilling Program
IPEV French Polar Institute
IPY International Polar Year

LC-MS Liquid Chromatography-Mass Spectroscopy

ME Maintenance Energy
MPa Megapascal

NAC NASA Advisory Council
NASA National Aeronautics and Space Administration
NDELA Nitrosodiethanolamine
NGRIP North Greenland Ice Core Project
NIPR National Institute of Polar Research
NPOC Non-purgeable Organic Carbon
NPR NASA Procedural Requirement
NRC National Research Council
NSF National Science Foundation
NTU Nephelometric Turbidity Unit

ODP Ocean Drilling Program
OPP Office of Polar Programs

PFT Perfluorocarbon Tracer
PNRA National Research Program in Antarctica
POC Particulate Organic Carbon
PP Planetary Protection
PPP Panel on Planetary Protection
PVC Polyvinyl Chloride

RCB Rotary Core Barrel
RES Radio-Echo Sounding
ROS Reactive Oxygen Species

Page 163

��� APPENDIX C

ROV Remotely Operated Vehicle

SALE Subglacial Antarctic Lake Exploration
SALEGOS Subglacial Antarctic Lake Exploration Group of Specialists
SAR Synthetic Aperture Radar
SCAR Scienti�c Committee on Antarctic Research
SRP Scienti�c Research Plan
SSB Space Studies Board

TDS Total Dissolved Solids
T-RFLP Terminal Restriction Fragment Length Polymorphism

UNITED Uni�ed Team for Exploration and Discovery
U.S. SALE U.S. Subglacial Lake Environments

WAIS West Antarctic Ice Sheet

Similer Documents