Frontiers in Polar Biology in the Genomic Era (2003) / Chapter Skim
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2. Important Questions in Polar Biology
2. Important Questions in Polar Biology
Pages 25-81
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From page 25... ...
The fascination that polar ecosystems hold for scientists thus is not difficult to understand. The "novel" or "exotic" nature of many polar organisms cannot fail to spike the curiosity of any biologist interested in how organisms "work" and how they have evolved in the extremes posed by high latitudes.
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From page 26... ...
light levels will affect polar ecosystems, we must characterize more fully the environmental impacts of these changes on polar organisms at all levels of biological organization: ecology and physiology to biochemistry and molecular biology. Furthermore, because the potential effects of global change on polar ecosystems may be severe, the implications for people living at high latitudes also have to be addressed.
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From page 27... ...
Though polar oceans are cold, they can be "hot spots" of evolution. Key Questions Given the distinct glacial histories of the Arctic and the Antarctic, the following questions may be asked:
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From page 28... ...
Because they evolved in highly stable environments, some polar species may be among the most stenotolerant organisms in the biosphere. For instance, Antarctic notothenioid fishes are the most stenothermal animals known; they die of heat death at temperatures above 4°C (Somero and DeVries, 1967)
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From page 29... ...
Other recent studies have shown that genes encoding the oxygen transport proteins hemoglobin and myoglobin have become dysfunctional in certain Antarctic notothenioids, the icefishes (see Plate 2; family Channichthyidae [Cocca et al., 1995; Sidell et al., 1997; Zhao et al., 1998~. These are the only vertebrates known to lack oxygen-binding transport proteins (Plate 3, Figure 2-1~.
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From page 30... ...
, suggesting that stenothermy may be a widespread characteristic of all taxa of polar organisms in both Antarctic and Arctic oceans. However, the loss of abilities to cope with increases in temperature may differ between organisms in the Antarctic and the Arctic Oceans.
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From page 31... ...
Understanding these regulatory cascades will add to our understanding of how gene expression in vertebrates is regulated in response to environmental change. Macromolecular antifreezes and ice-nucleating agents in terrestrial invertebrates, including insects, spiders, mites, nematodes, and many other organisms, especially sea-ice algae and other psychrophilic microorganisms, also merit additional study (Wharton and Worland, 1998~.
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From page 32... ...
Are there other instances that genes have been recruited for a new function, in order to allow organisms to adapt to polar conditions? What lessons about molecular evolution can be learned from studying the generation of new genetic capacities in polar organisms?
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From page 33... ...
As is clear from the information given above, recent exploitation of the tools of genome sciences in the study of polar organisms has led to many appealing examples of novel mechanisms of adaptation and has opened the door to exciting new lines of study. Thus, it is clear that the information obtained to date through application of genome sciences represents but the very "tip of the iceberg" in terms of what knowledge can be obtained through expansive use of genomic methods, including those of genomics, proteomics, and metabolomics, in the arena of polar biology.
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From page 34... ...
How Do the Transcriptomes, Proteomes, and Metabolomes of Polar Organisms Compare to Those of Other Species? Genome sequencing projects with polar species should be complemented by studies of changes that occur in the transcriptome and the proteome in response to environmental change.
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From page 35... ...
Microarray studies thus could point to the lesions that limit polar organisms' abilities to acclimate to environmental change, thereby further clarifying the threats that environmental change pose to these species. As the study of myoglobin production in icefishes has demonstrated, lesions in protein production may lie in events downstream from transcription.
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From page 36... ...
"-omic" Approaches Portend Progress in Basic and Applied Research One of the recurring themes of this report is that a fully integrated understanding of polar organisms will be possible by applying appropriate combinations of genomic, proteomic, and metabolomic approaches. This new appreciation of the biology of polar species will contribute critical new information about the "basic" biology of these organisms (for example, their evolution, their biogeography, and their capacities for responding to environmental change)
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From page 37... ...
Key Question · Do polar organisms produce unique organic molecules that could be exploited in biotechnological and biomedical contexts, for example, in maintaining living systems at low temperatures? Ice Museums: Do We Have a Record of Evolution and Reintroduced Genomes?
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From page 38... ...
· Based on sequence information from ancient DNAs, how rapidly has evolution occurred in polar organisms? · Are polar environments truly reservoirs of paleogenes that can accelerate the evolution of present day species through lateral gene transfer?
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From page 39... ...
Results from evolutionary and demographic studies using DNA from organisms frozen in permafrost contribute to our understanding of how climatic and other environmental changes during the last glaciation have affected life on our planet. Key Questions · What mechanisms of freezing tolerance do these organisms encode?
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From page 40... ...
Psychrophilic and psychrotolerant isolates originate from locations ranging from aquatic and marine ecosystems to terrestrial soils and glacial ice, with little in common except that all are permanently cold or frozen. The wide geographic distribution of related species from diverse frozen environments implies that clades of these bacterial genera evolved under cold circumstances and likely possess similar strategies to survive freezing and to remain active at low temperature.
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From page 41... ...
Key Questions · What is the evolutionary origin of the organisms present in the polar ice caps and glaciers? · If the microorganisms present in ice caps and glaciers are metabolically active, do they possess novel metabolic and biochemical pathways?
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From page 42... ...
Subglacial Lakes Antarctic subglacial lakes remain one of the last unexplored repositories of genetic information on our planet. More than 100 subglacial lakes have been identified with the largest (~14,000 km2; >1,000 m deep)
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From page 43... ...
When examined across taxa, rates of genetic exchange between populations of related polar organisms are likely to differ depending on dispersal mechanisms or routes of exchange. As a result, speciation and endemism are likely to differ greatly between major categories of organisms, directly affecting the biodiversity of polar ecosystems.
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From page 44... ...
Thus, the Arctic ecosystem is highly sensitive to shifts in the plant community at all levels, including both growth form, individual species, and possibly even genetic variation within species. Predicting how Arctic ecosystems will respond to environmental change requires a better understanding of the functional roles of different plant species and their specific responses to various environmental features.
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From page 45... ...
, raise many questions, including several at the population level that could benefit from genomic approaches. Have environmental changes led to genetic changes in the populations, for instance?
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From page 47... ...
Hence, characterization of polar soil microbial diversity will help the identification of microorganisms that are effective for various bioremediation activities. Key Questions · How does soil biodiversity vary over a polar latitudinal gradient?
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From page 48... ...
Prokaryotes provide a unique challenge to ecologists and biogeographers. Because they are difficult to culture, little is known about speciation, physiological function, or composition of microbial communities found in the two polar oceans.
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From page 49... ...
Inferences about speciation and the distribution of uncultured prokaryotes are now being made from ssu gene sequences (Delong et al., 1994; Murray et al., 1998, 1999; Hollibaugh et al., 2002~. An example of this kind of analysis is shown in Figure 2-3, where denaturing gradient gel electrophoresis was used to obtain a "fingerprint" of bacterial communities found at different locations in the Arctic Ocean (Bang and Hollibaugh, 2002~.
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From page 50... ...
to show how the composition of the bacteria community varies with depth, time, and location in the Arctic Ocean. Arrows and boxes denote bands that correspond to longer cloned fragments and bands that were excised and sequenced, respectively.
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From page 51... ...
Essentially all of the work to date in microbial genomics has been focused on prokaryotes that can be grown in pure culture or in association with host cells in culture. However, the advancement of genomic technologies makes possible the examination of microbial communities through DNA sequence and microarray analysis without the need for a pure culture as a starting point (Bela et al., 2000; 2002a; Rondon et al., 2000~.
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From page 52... ...
display? · What unique adaptations to their environment do polar organisms · What is the relationship between sea-ice microbial communities and those in the underlying seawater and sediments?
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From page 53... ...
POLAR PHYSIOLOGY AND BIOCHEMISTRY How Does Living at Extremely Low Temperatures Affect Metabolism and the Cost of Life? As early as the nineteenth century, natural historians reported that polar marine ectotherms exhibited surprisingly high rates of activity despite their low body temperatures.
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From page 54... ...
One question focuses on the intrinsic properties of biomolecules (nucleic acids, proteins, membrane lipids, etc.) and asks about the types of adaptations in these molecules that enable them to function satisfactorily at low temperatures where warm-adapted biomolecules are apt to fail.
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From page 55... ...
Lowered costs of living may arise not only from low temperatures per se but also from the extreme thermal stability of polar oceans. Stable thermal environments are likely to reduce energy costs because they preclude the necessity of carrying out temperature-acclimatory shifts in the transcriptome and proteome, which are required of ectotherms from thermally variable habitats if their cells are to contain the appropriate types and concentration of proteins and to conduct acclimatory restructuring of lipid-containing structures such as cellular membranes (Hochachka and Somero, 2002~.
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From page 56... ...
Insights into ways of reducing cellular energy demands might be helpful in designing protocols for improving the longevity and physiological state of cells and organs stored at low temperatures. The strategies used by polar species for reducing energy costs might serve as the basis for new approaches to cryopreservation.
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From page 57... ...
· How will global warming increase costs of living for polar organisms and what will be the consequence of these effects on polar ecosystems? · Can the adaptations used by polar organisms to reduce their energetic costs be exploited in biotechnology, for example, in cold preservation (cryopreservation)
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From page 58... ...
have shown that the catalytic rate constant kcat of the skeletal muscle isoform of Antarctic notothenioid fishes is four to five times greater than that of mammalian, avian, and thermophilic reptilian orthologues, when each was measured at 0°C. Furthermore, kcat varies in a regular, negative relationship with temperature among fishes, further supporting the hypothesis that the interspecific differences reflect evolutionary adaptation to different thermal regimes.
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From page 59... ...
Further study of enzymes from polar organisms should continue to provide significant new insights into macromolecular structure and function. Key Questions · Can the proteins of polar organisms teach us general rules about the mechanisms used to alter protein structural stability?
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From page 60... ...
· Does cold adaptation of molecules differ in steno- and eurythermal polar organisms, and if so, how? Physiological and Biochemical Responses to Abiotic Environmental Stresses As alluded to earlier, the general question of how organisms cope with the abiotic (physical and chemical)
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From page 61... ...
Although there is not much information about how polar organisms tolerate abiotic stresses, studies with organisms from temperate environments are yielding important insights into stress tolerance mechanisms that provide a framework for studying polar organisms. For example,
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From page 62... ...
Whether plants from the polar environments have low-temperature pathways related to the CBF pathway and, if so, whether the genes that comprise the CBF regulons are the same as those in Arabidopsis or include genes with more potent activities can be addressed through the application of genomic technologies. A low-temperature response that is conserved in bacteria is the "coldshock" response (Weber and Marahiel, 2002; Yamanaka, 1999~.
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From page 63... ...
In plants, bacteria, and other organisms, drought-induced genes also encode enzymes involved in the synthesis of low-molecular-weight compatible solutes such as praline, glycine, betaine, and sugar alcohols that have important roles in both osmotic adjustment and protecting membranes and proteins against damage due to low water potentials (Chen and Murata, 2002; Rontein et al., 2002~. Given the extreme nature of the low water availability in the Dry Valleys and many other places in the Arctic and Antarctic, the question arises as to whether the organisms present in these environments have protective mechanisms similar to those described for organisms that inhabit temperate regions or whether they have evolved additional novel mechanisms.
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From page 64... ...
Some of the key questions that can be addressed by genomic technologies are as follows: · What sensing and regulatory pathways have polar organisms evolved to cope with the dramatic fluctuations in abiotic environmental conditions that occur regularly in the Artic and Antarctic? · Do polar plants, for instance, have low-temperature pathways related to the CBF pathway; and if so, do they include novel genes or genes with more potent activities?
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From page 65... ...
Further development of these approaches offers great promise for better understanding functional relationships in complex microbial communities. Two factors that are consistently implicated as limiting factors for heterotrophic polar soil communities are temperature (Bunnell et al., 1977; Hobble, 1996; Schimel and Clein, 1996)
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From page 66... ...
· What is the reason for, or significance of, the great diversity in most microbial communities?
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From page 67... ...
Genomic and proteomic analysis of these communities would reveal the organisms involved and provide important information on the related processes that control their composition and productivity. Key Questions · What organisms constitute the microbial aggregates?
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From page 68... ...
Annual partial melting of the ice caps might then provide conditions compatible with active life or at least provide water in which these microorganisms may be preserved by subsequent freezing (Clifford et al., 2000; McKay and Stoker, 1989~. We can evaluate such hypotheses by analysis of polar ecosystems, but assessment of their validity will depend, ultimately, on scientific missions to explore and study the frozen surface of Mars.
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From page 69... ...
Wintertime Arctic sea ice, where liquid brines exist at temperatures of -35°C, provides a marine model for exploring the limits of life on this planet of relevance to Europa's saline, ice-covered ocean (Deming, 2002~. Key Questions · How does the combination of high pressure and low temperature in deep Antarctic lakes or the deep Arctic basins influence microbial survival and activity?
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From page 70... ...
PCR primers to the rest of the genome and, thus, to the additional genetic capability; and (2) developing robust probes and primer sets that can be used to detect poorly conserved genes encoding proteins that participate in important biogeochemical reactions.
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From page 71... ...
_ Q o ~n ~o . z y o o o z FIGURE 2-5 Phylogenetic tree constructed from sequences of cloned ssu rRNA genes showing the relationship of Arctic and Southern Ocean p-proteobacterial ammonia-oxidizing bacteria (AOB)
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From page 72... ...
In the context of polar biogeochemistry, undersampled habitats that might lead to the discovery of novel organisms are deep Arctic waters, nepholoid (particlerich) waters, Dry Valley lakes and soils, subglacial lakes, ice cores, and other polar soils.
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From page 73... ...
Recently, the efficacy of HTC was validated by its use for the isolation of members of the ubiquitous SARll marine bacterioplankton clade, organisms of global significance that previously had eluded cultivation (Figure 2-5; Rappe et al., 2002~. Key Questions · Is there a relationship between composition and biogeochemical function in polar microbial communities?
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From page 74... ...
The impact of elevated UV-B has been documented most extensively for the primary producers of polar marine ecosystems (de Mora et al., 2000; Neale et al., 1998; Smith et al., 1992; Prezelin et al., 1994; Smith et al., 1994; Weller and Penhale, 1994~. Primary productivity in the Southern Ocean declines by as much as 15 percent in areas affected by the ozone hole (Smith et al., 1992)
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From page 75... ...
. Cold temperatures may exacerbate the negative impact of UV on populations of polar organisms because the enzymatic systems that repair UV-mediated DNA damage (sullen and Lesser, 1991; Lesser et al., 1994)
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From page 76... ...
Linkage of whole ecosystem studies to measurements of the molecular responses of individual species will be critical to understanding the trophic impacts of UV radiation (Mostajir et al., 2000, and references cited therein) and validating predictive ecosystem models (Day and Neale, 2002~.
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From page 77... ...
As the potential for introductions grows, genomic approaches will provide the tools necessary to trace the sources and the spread of invasive species in polar regions. Key Questions · How great are the risks from human-introduced species to polar ecosystems?
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From page 78... ...
Currently, major threats are facing salmon populations, and contemporary genomic methods are likely to prove useful for weighing these threats and predicting the future success or failure of salmon stocks. As discussed earlier in the section "How Does Living at Extremely Low Temperatures Affect Metabolism and the Cost of Life," salmon populations are seriously threatened by warming of the oceans (Welsh et al., 1998~.
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From page 79... ...
Key Question · How will global climate change affect the biogeography of polar organisms? Genomic Technologies to Monitor Stocks of Commercially Exploited Marine Organisms Genomic tools also have roles in assessing the impacts of humans on the world's fisheries.
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From page 80... ...
Examples of other issues in polar biology that may be addressed by genomic studies include: · Biological rhythms, ultradian, circadian, and circannual cycles of resident plants and animals in the Arctic and Antarctic. These regulatory systemsand their space persistence, mechanisms of entrainment, and physiological and behavioral functions are largely unstudied in polar organisms.
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From page 81... ...
the polar regions are one of the least studied and understood ecosystems; (2) genome research applied to polar biology would serve as a useful "test bed" for temperate and tropical regions (e.g., there are tens of thousands of tropical fishes but only about 250 in Antarctica)
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